Analysis of Large Affymetrix Microarray Data Sets

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.


News

Package: aroma.affymetrix

Version: 3.1.1 [2018-04-16]

SIGNIFICANT CHANGES:

o Package requires R (>= 3.2.0) and BioC (>= 3.1) both released in April 2015.

BUG FIX:

o Removed invalid 'break' statement in getAlleleProbePairs() for AffymetrixCdfFile.

CODE REFACTORING:

o Using indexByRow(dim(x)) internally since indexByRow(x) will soon be deprecated in matrixStats.

DEPRECATED AND DEFUNCT:

o Passing argument 'ram' to any of the doNnn() methods is now defunct and gives an informative error message. It has been given a warning since v2.8.4 (May 2013). Use setOption(aromaSettings, 'memory/ram', ram).

o Monocell CDF files named with a very very old "-monocell.cdf" suffix are now ignored. There has been an informative error that these are defunct since v 2.6.3 (October 2012).

Version: 3.1.0 [2017-03-23]

NEW FEATURES:

o Now file and object sizes are reported using IEC binary prefixes, i.e. bytes, KiB, MiB, GiB, TiB, ..., YiB.

o Now doNnn() methods can be called directly from the command line, e.g. Rscript -e aroma.affymetrix::doCRMAv2 --dataSet=HapMap270 --chipType=GenomeWideSNP_6

o Objects no longer report on memory (RAM) usage.

REFACTORIZATION:

o Used partial element name 'coef' instead of 'coefficients' for lm() fit.

BUG FIXES:

o Package used %<=% internally with was deprecated in future (>= 1.4.0).

o ROBUSTNESS: Some regular expression patterns used for locating files would match any symbol when it intended to match only a period.

o The International HapMap Project (http://www.hapmap.org/) is being retired and HTTP server http://hapmap.ncbi.nlm.nih.gov/downloads/raw_data/ is decomissioned. System test scripts updated to download HapMap CEL files from the FTP server ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/ instead.

DEPRECATED AND DEFUNCT:

o Methods bgAdjustRma(), bgAdjustOptical() and bgAdjustGcrma() for AffymetrixCelFile as well as bgAdjustGcrma() for AffymetrixCelSet are now defunct.

Version: 3.0.0 [2016-01-09]

SIGNIFICANT CHANGES:

o Package requires R (>= 3.1.2) and BioC (>= 3.0) both released in October 2014.

NEW FEATURES:

o REPRODUCIBILITY: GcRmaBackgroundCorrection(), LimmaBackgroundCorrection(), and RmaBackgroundCorrection() gained argument 'seed'.

o REPRODUCIBILITY: Several of the methods now generate *.md5 checksum files for the data files they output.

o Now also convertToUnique() acknowledge asterisk tags.

PERFORMANCE:

o SPEED: Adding support for parallel/distributed processing via futures to some of the methods for which it is possible to process each sample independently, e.g. background and crosstalk correction methods.

REFACTORIZATION:

o ROBUSTNESS: Using do.call(fcn) internally instead of do.call("fcn").

o CLEANUP: Warnings on "is.na() applied to non-(list or vector) of type 'NULL'" are no longer generated.

SOFTWARE QUALITY:

o ROBUSTNESS: MatNormalization did not create CEL files atomically.

BUG FIXES:

o LimmaBackgroundCorrection(..., addJitter=TRUE) gave an error.

DEPRECATED AND DEFUNCT:

o CLEANUP: Formally defunct'ed bgAdjustRma(), bgAdjustGcrma(), bgAdjustOptical() for AffymetrixCelFile/AffymetrixCelSet since they have effectively been defunct'ed in the public API for years. These are now all incorporated in corresponding BackgroundCorrection classes.

Version: 2.14.0-9000 [2015-12-23]

o ROBUSTNESS: Using getPathname() instead of accessing private field.

BUG FIXES:

o convertToUnique() for AffymetrixCelSet would give an error if there was an error while checking if results already exist.

Version: 2.14.0 [2015-10-24]

o AvgPlm, used by for instance doCRMAv2(), would give harmless warning "Argument 'centers' for matrixStats::rowMads() has been renamed to 'center'. Please update code accordingly."

o ROBUSTNESS: fitCnProbes() for UnitModel could in rare cases give an error on one of the internal sanity checks.

SOFTWARE QUALITY:

o ROBUSTNESS: Explicitly importing core R functions.

BUG FIXES:

o extractAlleleSet() for SnpChipEffectSet now needs to load namspace 'oligoClasses' explicitly.

o writeCdf() for AffyGenePDInfo gave "Error in affxparser::writeCdf(...) : unused argument (pathname = ..." due to a bug/typo introduced in 2.13.2. Thanks to Guillaume Devailly for reporting on this.

DEPRECATED AND DEFUNCT:

o Removed methods marked as defunct in v2.11.3 (Feb 2014).

Version: 2.13.2 [2015-05-26]

SIGNIFICANT CHANGES:

o Package now requires R (>= 3.1.1) released July 2014. This allows us to use BioC (>= 3.0) (October 2014).

SOFTWARE QUALITY:

o ROBUSTNESS: Many functions now assert that they don't return file data sets with duplicated entries.

o ROBUSTNESS: Package now declares all S3 methods.

Version: 2.13.1 [2015-01-23]

o Now a pre-existing monocell CDF can be recreated and overwritten using getMonocellCdf(cdf, force=TRUE).

BUG FIXES:

o getMonocellCdf() for AffymetrixCdfFile would throw "Error in (...) : 3 arguments passed to '(' which requires 1". This was due to a typo (erroneous newline) introduced in 2.13.0. Add package tests for this. Thanks to Qingzhou Zhang for reporting on this.

Version: 2.13.0 [2015-01-17]

o Bumped version for CRAN submission.

o Updated package dependencies.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

Version: 2.12.10 [2015-01-06]

o CLEANUP: Major cleanup of namespace imports from suggested packages such as affxparser and aroma.light.

Version: 2.12.9 [2014-11-17]

o Updated redundancy tests under testScripts/ to find rowMedians() of the matrixStats package. The matrixStats package used to be attached whenever aroma.light (< 2.1.1) was attached, but no longer.

Version: 2.12.8 [2014-09-04]

BUG FIXES:

o ROBUSTNESS/BUG FIX: createFrom(..., mode="copy") for AffymetrixCelFile would give an error on "No permission to modify existing file: ..." iff the source file had read-only permission. This bug was introduced by changes to base::file.copy() in R (>= 2.13.0) [April 2011]. Thanks to Taylor Raborn at Indiana University for reporting on this.

Version: 2.12.7 [2014-08-27]

BUG FIXES:

o Added forgotten NAMESPACE imports.

Version: 2.12.6 [2014-06-29]

BUG FIXES:

o getAromaCellSequenceFile() for AffymetrixCdfFile used undefined variable 'nbrOfCells'.

Version: 2.12.5 [2014-06-24]

SOFTWARE QUALITY:

o Added package system tests utilizing example data of Bioconductor package AffymetrixDataTestFiles, iff installed.

Version: 2.12.4 [2014-06-09]

SIGNIFICANT CHANGES:

o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were released April 2013 and are in fact old and it's recommended to use a more recent version of R.

o Added 'SuggestsNote' field to DESCRIPTION with list of packages that are recommended for the most common use cases.

o Bumped package dependencies.

Version: 2.12.3 [2014-05-02]

o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.

Version: 2.12.2 [2014-04-28]

o Added justRMA() for AffymetrixCelSet, which with good precision reproduces the results of the default setting of justRMA() in the affy package. It does so by still running with a constant memory profile. This means that a much larger number of samples can be processed using this implementation.

o doCRMAv2(..., drop=FALSE) and hence doASCRMAv2(..., drop=FALSE), did not return the base-position normalization step, although it was done and its outcome was part of all downstream steps.

o extractExpressionSet() for ChipEffectSet gained argument 'orderUnitsBy' and returns standard errors as well.

Version: 2.12.1 [2014-04-26]

o SPEEDUP: Minor speedup by replacing repetive ::() calls with repetive () calls; the '::' operator is fairly expensive. You should expect a small speed improvement when using MatSmoothing(), RmaPlm(..., flavor="oligo") and when calculating weights using ExonRmaPlm and QualityAssessmentModel, to name a few examples.

Version: 2.12.0 [2014-03-07]

o Bumped version for CRAN submission.

o Updated package dependencies.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

Version: 2.11.3 [2014-02-28]

o Now methods that supports searching sibling root directories do so by default. Previously this had to be explicitly enabled via an option.

DEPRECATED AND DEFUNCT:

o CLEANUP: Removed defunct methods. Made previously deprecated defunct.

Version: 2.11.2 [2014-01-04]

DEPRECATED AND DEFUNCT:

o CLEANUP: Dropped defunct methods '[' and '[[' for AffymetrixCelSet and CnagCfhSet (which have been defunct since 2013-04-29).

Version: 2.11.1 [2013-10-17]

o DOCUMENTATION: Minor tweaks to the help for the doNNN() methods.

Version: 2.11.0 [2013-10-17]

SIGNIFICANT CHANGES:

o Package now requires R (>= 2.15.0) [and Bioc (>= 2.10.0)].

o Updated package dependencies.

Version: 2.10.3 [2013-10-07]

o CLEANUP: No longer need to attach R.utils for backward compatibility.

o CLEANUP: Package no longer apply downloaded package patches.

o CLEANUP: Now explicitly importing only what is needed in NAMESPACE.

o CLEANUP: No longer uses ':::' for accessing 'oligo' functions.

o Updated package dependencies.

DEPRECATED AND DEFUNCT:

o CLEANUP: Deprecated patch() for AromaAffymetrix.

Version: 2.10.2 [2013-09-28]

o Now the 'aroma.affymetrix' Package object is also available when the package is only loaded (but not attached).

o Updated package dependencies.

Version: 2.10.1 [2013-08-21]

o Now explicitly importing R.filesets and aroma.core in NAMESPACE.

Version: 2.10.0 [2013-08-04]

o CLEANUP: The formal package dependency on Bioconductor packages 'aroma.light' and 'affxparser' has been relaxed so the package can be installed without them.

o CLEANUP: Package now only imports matrixStats, R.oo, R.filesets and aroma.apd.

o Bumped version for CRAN submission.

o Updated package dependencies.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

DEPRECATED AND DEFUNCT:

o CLEANUP: Removed since-long defunct methods. Made deprecated methods defunct.

Version: 2.9.7 [2013-07-28]

o ROBUSTNESS: byPath() for DChipDcpSet was not declared static.

BUG FIXES:

o In certain cases, calls to static method byPath() would be affected by the NextMethod() '...' bug reported in R-devel thread "Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?" on 2012-10-16.

Version: 2.9.6 [2013-07-03]

o Added argument 'flavor' or doRMA() making it easier to replicate the results of other packages, e.g. doRMA(..., flavor="oligo").

Version: 2.9.5 [2013-06-02]

o ROBUSTNESS: Now more methods are creating/writing signals atomically.

BUG FIXES:

o Since v2.9.0, doFIRMA() would give "Exception: Unknown arguments: .onUnknownArgs" in the alternative splicing step.

o calculateConfidenceScores() for CrlmmModel used defunct method isHeterozygote() instead of isHeterozygous().

o Certain methods could throw 'Error in UseMethod("getChecksum"): no applicable method for 'getChecksum' applied to an object of class "list"' if (and only if) R.cache package was not attached. The same bug was fixed on aroma.core v2.9.2 recently.

Version: 2.9.4 [2013-05-30]

o Now it's possible to call aroma.affymetrix::doRMA() without first loading package. Same for all other doNnn() methods, e.g. doCRMAv2(), doFIRMA() and doGCRMA().

Version: 2.9.3 [2013-05-25]

o SPEEDUP: Replaced all rm() calls with NULL assignments.

Version: 2.9.2 [2013-05-22]

o CLEANUP: Now using getChecksum() instead of (internal) R.filesets::digest2() with identical results.

o CLEANUP: Now getIdentifier() for CnagCfhFile utilizes getChecksum() for the GenericDataFile class.

Version: 2.9.1 [2013-05-20]

SOFTWARE QUALITY:

o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.

Version: 2.9.0 [2013-05-02]

o Submitted to CRAN.

SOFTWARE QUALITY:

o The package passes all redundancy tests.

Version: 2.8.4 [2013-05-02]

o DOCUMENTATION: Now doRMA(), doGCRMA(), doFIRMA(), doCRMAv1()/doASCRMAv1() and doCRMAv2()/doASCRMAv2() are fully documented and listed in the help index.

o Added argument 'annotationPkg' to extractExpressionSet() for ChipEffectSet, which (indirectly) sets the 'annotation' slot of the returned ExpressionSet.

o Added extractFeatureSet() for AffymetrixCelSet.

o SPEEDUP: Added ^Cyto.*Array$ to list of SNP chips that isSnpChip() for AffymetrixCdfFile knows of without having to scan the CDF.

o SPEEDUP: Just as doCRMAv2()/doASCRMAv2(), now also doRMA() and doGCRMA() return much quicker if already processed.

DEPRECATED AND DEFUNCT:

o CLEANUP: Removed argument 'ram' from doNnn() methods in favor setOption(aromaSettings, 'memory/ram', ram).

o CLEANUP: Made several deprecated methods defunct.

Version: 2.8.3 [2013-04-01]

o Force creation of a generic process(), because depending on the version of R.rsp at the time of the build, process() may be missing or not.

o Bumped up package dependencies.

Version: 2.8.2 [2013-03-22]

o Obscufated the error message on ASCII CDFs on how to change settings to allow the processing of such, because it shouldn't be easy to do that.

Version: 2.8.1 [2013-03-05]

o DOCUMENTATION: Updated the help usage section for all static methods.

o Bumped up package dependencies.

Version: 2.8.0 [2012-12-21]

o No updates.

o Bumped version for CRAN submission.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

Version: 2.7.9 [2012-12-21]

o Bumped package dependencies.

o Utilizing new startupMessage() of R.oo.

o ROBUSTNESS: Now all internal pathnames are shorter than 100 characters, which is the upper limit that 'tar' supports.

DEPRECATED AND DEFUNCT:

o Now using argument 'colClasses' (was 'colClassPatterns') for all readDataFrame():s and elsewhere.

Version: 2.7.8 [2012-12-18]

o ROBUSTNESS: Added argument 'unitsBy' (and 'namesBy') to writeCdf() for AffyGenePDInfo, where 'unitsBy' defaults to "transcript". It now also drops any duplicated probe entries. Furthermore, calling writeCdf() for other classes of DBPDInfo objects will now give a more informative error message that those classes are yet not supported. Thanks Guido Hooiveld (Wageningen University, Netherlands) for suggestions and tests.

o Now validate() for AffymetrixCdfFile accepts empty unit names as long as the unit is not empty.

BUG FIXES:

o writeCdf(..., useTranscriptCluster=FALSE) for AffyGenePDInfo could generate empty unit names files for units with 'fsetid' <= 9999.

Version: 2.7.7 [2012-12-10]

BUG FIXES:

o getTimestamp() for AffymetrixCelFile would throw an error if the CEL file header did not have a timestamp. Thanks Guido Hooiveld (Wageningen University, Netherlands) for reporting this.

Version: 2.7.6 [2012-12-06]

o ROBUSTNESS: Utilizing new getOneFile() internally.

Version: 2.7.5 [2012-12-01]

BUG FIXES:

o BUG FIX/ROBUSTNESS: convertToUnique() for AffymetrixCelSet would return all CEL files found in the output directory, not just the ones corresponding to the input set, and possibly in a different order.

Version: 2.7.4 [2012-11-29]

o DOCUMENTATION: Added help pages to more methods.

o ROBUSTNESS: updateUnits() for ResidualSet did not update the files in lexicographic order as previously claimed.

Version: 2.7.3 [2012-11-28]

o ROBUSTNESS: Added system test scripts for building UGP and UFL file from Affymetrix CSF and NetAffx CSV files for GenomeWideSNP_6.

BUG FIXES:

o Static allocateFromCdf() for AromaUfcFile and AromaUflFile would throw errors on "Cannot retrieve writable file/directory because it is NA.". This turns out to be related to the trap reported in R-devel thread 'Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?' on Oct 16, 2012. Thanks Ioana Cutcutache (Duke-NUS in Singapore) for reporting on this.

Version: 2.7.2 [2012-11-28]

o ROBUSTNESS: Added the FileCacheKeyInterface to all classes directly extending GenericDataFile and TabularTextFile.

o MEMORY: readUnits() for ChipEffectFile, FirmaFile, ParameterCelFile, ResidualFile, and WeightsFile no longer cache results in memory by default.

Version: 2.7.1 [2012-11-26]

o Lowered the package dependencies to aroma.light (>= 1.22.0) and affxparser (>= 1.26.4) so that this package can be easily installed on R (>= 2.14.0).

Version: 2.7.0 [2012-11-24]

o Bumped version for CRAN submission.

o Bumped up package dependencies.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

Version: 2.6.16 [2012-11-21]

o Updated verbose output of parameters.

Version: 2.6.14 [2012-11-21]

o DOCUMENTATION: Hiding more internal methods from the help indices.

o CLEANUP: Now utilizing the new ParametersInterface.

o CLEANUP: Replaced all getParameterSet() with getParameters().

o CLEANUP: bgAdjustGcrma() for AffymetrixCelSet no longer reads and write probe affinity files in the deprecated APD format.

o CLEANUP: Removed obsolete code from internal bgAdjustOptical() that was never reached and that loaded affinities via obsolete APD files.

DEPRECATED AND DEFUNCT:

o CLEANUP: bgAdjustOptical() and bgAdjustRma() for AffymetrixCelSet are now defunct. Instead, see OpticalBackgroundCorrection and RmaBackgroundCorrection.

o CLEANUP: Deprecated "[" and "[[" for AffymetrixCelFile, AffymetrixCelSet, CnagCfhFile, and CnagCfhSet.

Version: 2.6.13 [2012-11-18]

o Now package explicitly imports R.cache, because aroma.core is no longer loading it.

Version: 2.6.12 [2012-11-14]

o CLEANUP: getWeights() for QualityAssessmentModel no longer sets the alias of the returned data set, because the use of aliases is deprecated.

o CLEANUP: writeImage() for AffymetrixCelFile no longer supports sample name aliases.

Version: 2.6.11 [2012-11-13]

o CLEANUP: Properly declared all cached fields, making it possible to remove nearly all clearCache() implementations because the one for Object takes does the job.

Version: 2.6.10 [2012-11-12]

o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere. Similarly, seq(ds) where 'ds' is GenericDataFileSet is now replaced by seq_along(ds). Likewise, seq_len(x) replaces seq(length=x), and length(ds) replaces nbrOfFiles(ds).

Version: 2.6.9 [2012-11-08]

o Renamed getColumnNames() to getDefaultColumnNames() for all classes inheriting from GenericTabularFile, because of the new ColumnNamesInterface interface.

Version: 2.6.8 [2012-11-05]

o CLEANUP: Replaced all whichVector() with which(), because the latter is now the fastest again.

Version: 2.6.7 [2012-10-29]

o CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of filePath(..., expandLinks="any").

Version: 2.6.6 [2012-10-21]

o ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead of mkdirs(), because the former will do a better job in creating and asserting directories on slow shared file systems, and when it fails it gives a more informative error message.

Version: 2.6.5 [2012-10-18]

o ROBUSTNESS: Now createMonocellCdf() for AffymetrixCdfFile validates the CDF (via new validate()). This will give more informative error message in case the CDF is invalid, e.g. containing "empty" units.

o ROBUSTNESS: Added validate() for AffymetrixCdfFile, which validate a CDF for the most "common" errors, to help troubleshooting. Note that the validation is not complete, i.e. rare/unknown errors are not caught.

o Now as.character() for all AromaChipTypeAnnotationFile classes, and hence print(), reports the file size both as abbreviated as well as in exact number of bytes, e.g. "24.66 MB (25853850 bytes)" (used to only be "24.66 MB").

Version: 2.6.4 [2012-10-16]

BUG FIXES:

o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf. R-devel thread 'Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?' on Oct 16, 2012.

Version: 2.6.3 [2012-10-14]

o CLEANUP: Moved AromaUnitGcContentFile to aroma.core.

DEPRECATED AND DEFUNCT:

o CLEANUP: Removed several defunct/obsolete methods and turned deprecated methods into defunct/obsolete ones.

o CLEANUP: findByChipType() for AffymetrixCdfFile no longer support monocell CDF file named -monocell.CDF, and gives an informative error if that is still the case. Since December 2007, the filename should instead be ,monocell.CDF.

o CLEANUP: createParamCdf() for ChipEffectFile and FirmaFile no longer support '-monocell' filenames. If detected, an informative error is thrown.

Version: 2.6.2 [2012-09-15]

BUG FIXES:

o doCRMAv2() failed to quickly located already available results if the chip type of the CDF had tags, e.g. 'GenomeWideSNP_6,Full'.

Version: 2.6.1 [2012-09-14]

o MEMORY: Now getUnitIntensities() and readUnits() for AffymetrixCelSet no longer cache the results in memory if argument 'units' is NULL.

o CLEANUP: Restructured part of the test scripts tree. Added a new batch launcher.

BUG FIXES:

o BUG FIX/ROBUSTNESS: Although getUnitIntensities() for AffymetrixCelSet would retrieve the CDF tree structure and pass it to affxparser's readCelIntensities(), it was done in such a way that the latter would still need to find and read the CDF. This meant that it would not necessarily retrieve the same CDF as the AffymetrixCelSet used.

o The utility function for downloading individual CEL files from GEO would give an error that it could not gunzip the downloaded file, iff the filename extension was lower case, e.g. *.cel.gz instead of *.CEL.gz.

Version: 2.6.0 [2012-09-05]

o Submitted to CRAN.

SOFTWARE QUALITY:

o The package passes all redundancy tests.

Version: 2.5.11 [2012-09-05]

o ROBUSTNESS: Now doCRMAv1() adds also tag "v1" to the allele-specific calibration step. The reason for this is to differentiate it from the output of doCRMAv2(). NOTE: This update means that any old CRMAv1 analyzes will not be detected by doCRMAv1(); to have doCRMAv1() detect those add tag "v1" in that calibration step, e.g. "ACC,-XY,v1".

o ROBUSTNESS: Now the CrlmmModel constructor asserts that the chip effects were estimated without merging the strands (mergeStrands=FALSE). If not, an informative exception is thrown.

Version: 2.5.10 [2012-09-04]

SOFTWARE QUALITY:

o CLEANUP/ROBUSTNESS: Updated test scripts by rewriting some tests to be more clear/consistent on what they are testing and by cleaning out tests that duplicates each other etc.

o Added system test scripts that automatically download the needed test data sets and install some extra packages needed for some of the tests.

BUG FIXES:

o BUG FIX/ROBUSTNESS: extractAlleleSet(), extractSnpCnvQSet() and extractSnpQSet() for SnpChipEffectSet would throw an exception iff the 'Biobase' package was not loaded.

Version: 2.5.9 [2012-08-31]

SOFTWARE QUALITY:

o Added system test scripts that automatically download the needed annotation data files iff missing. This simplifies running the package's system tests on a new system.

Version: 2.5.8 [2012-08-30]

o CLEANUP: Package no longer masks boxplot.stats(), getPackageName() and write() from other packages.

o CLEANUP: Dropped system tests that did not test what other tests already test.

DEPRECATED AND DEFUNCT:

o CLEANUP: Dropped readCdfDataFrame(), which is identical to the one in affxparser, which has remained the same since affxparser v1.21.1 (Oct 2010).

Version: 2.5.7 [2012-08-28]

o SPEED UP: Now doCRMAv2() returns even faster if already processed.

SOFTWARE QUALITY:

o Added systems test for running doASCRMAv2() in parallel using parLapply().

Version: 2.5.6 [2012-08-21]

o CLEANUP: getRlmFitFunctions() no longer falls back to affyPLM, which was really only needed back in 2007.

DEPRECATED AND DEFUNCT:

o CLEANUP: Dropped support for obsolete RmaPlm(..., flavor="affyPLMold").

o CLEANUP: Now RmaPlm(..., flavor="oligo") no longer supports oligo (< 1.7.19), which can be considered obsolete version by now.

Version: 2.5.5 [2012-08-18]

o Added argument 'useTranscriptCluster' to writeCdf() for AffyGenePDInfo.

Version: 2.5.4 [2012-06-21]

o CLARIFICATION: Restructured the bpmapCluster2Cdf() method such that is more clear how BPMAP sequences are filtered out, i.e. keeping sequencing with a matching group name and excluding those that appears to be non-genomic control sequences.

o ROBUSTNESS: Arguments 'rows' and 'cols' for bpmapCluster2Cdf() are mandatory (again). The reason for this is that the BPMAP file is only useful to infer a lower bound for them, but not their exact values.

o Added argument 'path' to bpmapCluster2Cdf(), which now defaults to annotationData/chipTypes//.

BUG FIXES:

o bpmapCluster2Cdf() would exclude all units that had a probe starting at the very first position of a BPMAP sequence, because it interpreted that (incorrectly) as being a non-genomic control sequence. This made no difference on some tiling arrays, but for others it dropped almost everything in the BPMAP file, e.g. Dm_tiling2_MR_v01.bpmap. Thanks Hanat T, Heidelberg for reporting.

o bpmapCluster2Cdf(..., minNbrOfProbes=n) filtered out units with less than (n+2L) probes, not n probes as documented.

o bpmapCluster2Cdf() would write the incorrect 'unitnumber' in the CDF units (it was using the BPMAP sequence index). This bug should have no impact on analysis in the Aroma framework, because that CDF field is ignored.

Version: 2.5.3 [2012-06-18]

o FIX: Fixed a typo in an error message generated by byChipType() for AromaChipTypeAnnotationFile.

Version: 2.5.2 [2012-06-15]

o Now writeCdf() for AffyGenePDInfo returns the pathname of the CDF.

o Added trial version of class AffymetrixPgfFile.

SOFTWARE QUALITY:

o ROBUSTNESS: Added a full system test for CalMaTe.

Version: 2.5.1 [2012-03-28]

o Now convertToUnique() for AffymetrixCelSet skips already processed files in partially processed data sets. Previously it would give an error if only some output files existed.

Version: 2.5.0 [2012-03-25]

o Submitted to CRAN.

SOFTWARE QUALITY:

o The package passes all redundancy tests.

Version: 2.4.3 [2012-03-23]

o CRAN POLICY: Package no longer utilizes .Internal() calls.

DEPRECATED AND DEFUNCT:

o CLEANUP: Deprecated PdInfo2Cdf() in favor (identical) pdInfo2Cdf(), because the former does not follow the Aroma naming conventions.

Version: 2.4.2 [2012-03-06]

o GENERALIZATION: The new ArrayExplorer v3.4 will work with most commonly used web browsers including Mozilla Firefox, Google Chrome, Microsoft Internet Explorer, Apple Safari, and Opera.

o CRAN POLICY: Started to remove .Internal() calls.

Version: 2.4.1 [2012-01-14]

o ROBUSTNESS: Now the fit function of MbeiPlm gives an error whenever one tries to use prior parameters, which are yet not supported.

o Updated getFitUnitGroupFunction() for RmaPlm to support prior probe-affinity parameters.

o Added argument 'listOfPriors' to MultiArrayUnitModel(). Such priors are passed to the internal fitUnit() method.

o Now validate() of MultiArrayUnitModel accepts single-array data sets, iff priors are set.

Version: 2.4.0 [2012-01-11]

o ROBUSTNESS: Updated package dependencies.

SOFTWARE QUALITY:

o Adapted a few redundancy tests for the most recent updates.

BUG FIXES:

o fit() for ProbeLevelModel would throw an error due to a sanity check on unit dimensions that was only valid in certain cases.

Version: 2.3.5 [2011-11-20]

o SPEEDUP: Constructor for AllelicCrosstalkCalibration no longer calls the very slow hasUnitTypes() for AffymetrixCdfFile, but instead only the much faster getUnitTypes().

o Now byChipType() for AromaChipTypeAnnotationFile gives an error message with more information on which file it failed to locate, e.g. by specifying filename extension it looked for.

o Added abstract getDefaultExtension() for AromaChipTypeAnnotationFile.

BUG FIXES:

o Internally justSNPRMA() for AffymetrixCelSet would pass argument 'verbose=log' instead of 'verbose=verbose', which would throw an error unless 'log' was assigned to be a logical value or a Verbose object.

DEPRECATED AND DEFUNCT:

o CLEANUP: Deprecated doCRMA(). Use doCRMAv1() or doCRMAv2() instead.

Version: 2.3.4 [2011-11-18]

o Now fit() for ProbeLevelModel fits one type of units at the time, which in turn is fitted in chunks of units with equal number of groups and cells per groups (very small chunks are merged together). Doing so will eventually allow us to speed up the restructuring of the data when reading signals and writing parameter estimates.

o ROBUSTNESS: Added validation of argument 'fields' to readRawData() of AffymetrixCelFile and more internal sanity checks in that method.

Version: 2.3.3 [2011-11-11]

o Now fit() for ProbeLevelModel fits one type of units at the time. For each unit type, the fitting is done in chunks. The timing statistics presented in the verbose output is now per unit type. The purpose of this is to move toward fitting in chunks of units where the units are all of the same type and dimension (number of groups and number of cells per group).

SOFTWARE QUALITY:

o Added more system tests.

Version: 2.3.2 [2011-11-10]

o Added doFIRMA().

o ROBUSTIFICATION: Now FirmaModel(plm) asserts that 'plm' is an ExonRmaPlm object (before any ProbeLevelModel would work), and that the PLM is setup for transcripts (mergeGroups=TRUE), not exons.

o SPEEDUP: Now the internal fit functions of FirmaModel utilizes the 'matrixStats' package. Also cleaned out some unnecessary calls.

o ROBUSTNESS: doGCRMA() is now guaranteed to undo any changes of the CDF of the data set, e.g. if there is a user interrupt.

Version: 2.3.1 [2011-11-05]

o FIX: The verbose enter/exit statements of fit() of CrlmmModel() did not match up, resulting deeper and deeper indentations.

Version: 2.3.0 [2011-10-28]

o Added a namespace to the package, which will be more or less a requirement starting with R v2.14.0.

o Added Bioconductor package 'AffymetrixDataTestFiles' to the list of suggested package, just to remove one R CMD check "NOTE".

Version: 2.2.3 [2011-09-29]

SOFTWARE QUALITY:

o Added more system tests.

Version: 2.2.2 [2011-09-17]

o Added writeCdfByExcludingCells() for AffymetrixCdfFile.

Version: 2.2.1 [2011-09-11]

o Added createExonByTranscriptCdf() for creating exon-by-transcript CDFs. This methods was adapted from the createTranscriptCDF(), which was previously provided online.

o Added a build script for createExonByTranscriptCdf() on HuEx-1_0-st-v2.

o Added getHeaderAttributes() for AffymetrixNetAffxCsvFile which is used by new getGenomeBuild(), getNetAffxBuild() and getNetAffxDate().

Version: 2.2.0 [2011-09-01]

o Submitted to CRAN.

SOFTWARE QUALITY:

o The package passes all redundancy tests.

Version: 2.1.9 [2011-08-31]

o Added bpmapCluster2Cdf(), which is a pruned and robustified version of ditto previously provided by Mark Robinson online. This new version includes more sanity checks and avoids overwriting existing CDF files.

o ROBUSTNESS: Now env2Cdf() writes the CDF file atomically by first writing to a temporary file which is then renamed. It now also returns the pathname to the CDF written.

BUG FIXES:

o ROBUSTNESS: getTimestamp() for AffymetrixCelFile would throw "Error in if (hasTimestamp) { : argument is of length zero" if the CEL file had a DAT header with a non-standard chip type string, e.g. an early-access label or no label at all. Updated the local/inner getTimestampFromDatHeader() of getTimestamp() to also handle such CEL files. Thanks Irina Ostrovnaya at MSKCC for reporting on this.

Version: 2.1.8 [2011-08-16]

o ROBUSTNESS: If static byName() for AffymetrixCelSet fails to setup a data set, it now reports the error message for each data set directory it tried.

Version: 2.1.7 [2011-08-08]

o WORKAROUND: Added similar workarounds as in v2.1.6 for more methods defined in aroma.core, apply(), rowSums() etc.

Version: 2.1.6 [2011-07-27]

o WORKAROUND: In order for the package to work with the most recent version of R devel, which automatically add namespaces to packages who do not have one, we explicitly have specify that this package should get function such as cat() and getOption() from R.utils (instead of 'base').

Version: 2.1.5 [2011-07-24]

o Bumped up the package dependencies, especially since R will soon (in practice) require namespaces for all packages.

Version: 2.1.4 [2011-07-14]

o Added extractExpressionSet() for ChipEffectSet.

o ROBUSTNESS: Added redundancy tests for doRMA() and extractExpressionSet() for the HG-U133_Plus_2 chip type.

Version: 2.1.3 [2011-06-07]

o ROBUSTNESS: Now the search path is adjusted such that 'ggplot2' comes after 'aroma.affymetrix', because the former overrides the generic rescale() function of the latter with a non-generic function.

Version: 2.1.2 [2011-05-26]

o Added an archive of scripts used to build ACS, UGP and UFL annotation files. The archive is located under buildScripts/ of the package installation directory and sorted by chip types.

Version: 2.1.1 [2011-04-18]

o DOCUMENTATION: Added more help to createUniqueCdf() for AffymetrixCdfFile.

o More updates to readGeneAssignments() for AffymetrixNetAffxCsvFile.

DEPRECATED AND DEFUNCT:

o DEPRECATED: getUnique() and createUnique() are deprecated. Use getUniqueCdf() and createUniqueCdf() instead.

o CLEANUP: Dropped argument 'sep' of createMonocellCdf() and createUniqueCdf() for AffymetrixCdfFile.

Version: 2.1.0 [2011-04-08]

o No updates. Submitted to CRAN.

Version: 2.0.10 [2011-04-07]

o Added argument 'drop' to doRMA(), doGCRMA(), doCRMAv1(), and doCRMAv2(). If FALSE, all intermediate data sets and models are returned in a named list, otherwise only the final data set(s).

o Added argument 'uniquePlm' to doRMA() and doGCRMA() for doing probe-level summarization on unique probe sets only.

o Added readGeneAssignments() for AffymetrixNetAffxCsvFile.

o CLEANUP: Utilizing hpaste() internally wherever applicable.

SOFTWARE QUALITY:

o Package passes all system tests.

Version: 2.0.9 [2011-03-26]

o ROBUSTNESS: Now internal bgAdjustGcrma(..., type="affinities") for AffymetrixCelFile gives a more informative error message when there are too few negative controls.

Version: 2.0.8 [2011-03-14]

o doRMAv1() and doCRMAv2() gained argument 'lengthRange', which is passed to the constructor of FragmentLengthNormalization.

o SPEEDUP: Added MOUSEDIVm520650 to the set of predefined chip types in AllelicCrosstalkCalibration.

Version: 2.0.7 [2011-03-10]

BUG FIXES:

o append() for AffymetrixCelSet:s would throw 'Error in base::append( this$files, files, ...) : unused argument(s) (other = NA)'. Added a redundancy test. Thanks Ajanthah Sangaralingam at Queen Mary, University of London, for reporting on this.

Version: 2.0.6 [2011-03-04]

o ROBUSTNESS: Now getCellIndices() for AffymetrixCdfFile asserts that argument 'units' can be coerced to integer indices. Also, after correcting a bug in lapplyInChunks() of aroma.core, getCellIndices() now correctly returns an empty set if argument 'units' is integer(0).

Version: 2.0.5 [2011-03-03]

o GENERALIZATION: Now AffymetrixCelSet and CnagCfhSet locates sample annotation files and sets the attributes following the new aroma search convention, i.e. by first loading *.saf files from main root path annotationData/ and then from optional sibling root paths annotationData,/.

o ROBUSTNESS: QuantileNormalization now saves normalized data atomically, which lowers the risk for generating incomplete/corrupt data files.

o ROBUSTNESS: Added a return contract/sanity check asserting that getUnitsOnChromosomes() for GenomeInformation truly returns valid 'unit' indices. Thanks to Emilie Sohier, France for reporting on a problem related to this.

Version: 2.0.4 [2011-03-01]

o GENERALIZATION: Now getAverageFile() and getBaseline() first try to locate an existing result file in one of the root paths. If not found, a new one is created.

o GENERALIZATION: Now byName() for AffymetrixCelSet tries to setup all data set directories matching the query and not just the first one. It also requires that the data sets found by byPath() are non-empty, otherwise they are skipped.

o STANDARDIZATION: Now the default output path for all allocateFromCdf() is annotationData/chipTypes//. Before it was the same directory as the CDF, which may for instance have been in a deeper subdirectory, or recently also in a sibling root path.

o CLEAN UP: Harmonized all code for allocating/writing atomically, where we first write to a temporary file which is then renamed.

Version: 2.0.3 [2011-02-24]

o GENERALIZATION: Starting to add support for locating data sets in root paths that also have tags, e.g. rawData/ and rawData,shared/. When this is in place, it will simplify sharing of data sets, intermediate and final results, which in turn will help multiple users avoiding reprocessing the same data sets.

o Now getAverageFile() for AffymetrixCelSet and DChipDcpSet, as well as getBaseline() for ChipEffectSet drop tags from the output root path before creating the file. Likewise, the target distribution file generated by QuantileNormalization is created in a root path without tags. Currently, this requires that aroma setting 'devel/dropRootPathTags' is TRUE.

o Added findTargetDistributionFile() to QuantileNormalization for locating an existing target-distribution file. The previously used getTargetDistributionPathname(), which returns a hardwired pathname, is now only used for creating a target-distribution file (in a root directory without tags).

o Now convertToUnique() for AffymetrixCelSet searches for already available data sets using the aroma-wide search rules. Before it assumed it would always be located in probeData/, but with the new rules it can also be in probeData,/.

o ROBUSTNESS: getTimestamp() for AffymetrixCelFile no longer assumes that the file's DAT header contains a timestamp and tries to translate. Instead it first tests for the timestamp pattern, and returns NA if not found.

Version: 2.0.1 [2011-02-20]

o KNOWN ISSUE: install.packages("aroma.affymetrix") does not work because the package depends on the 'affxparser' package which has to be installed from on Bioconductor. For now, the DESCRIPTION file has been updated with installation instructions.

DEPRECATED AND DEFUNCT:

o CLEANUP: Replaced calls to deprecated getListOfChipEffectSets() with getSets().

Version: 2.0.0 [2011-02-16]

o No updates. Submitted to CRAN.

Version: 1.9.5 [2011-02-15]

o CLEANUP/GENERALIZATION: Now all system tests for the Hs_PromPR_v02 chip type use public data sets. Before some of them used a private data set. Remaining data sets that are non-public and used in system tests:

  • GenomeWideSNP_6: TCGA,OV,testSet,pairs,Broad (1 test)

o HARMONIZATION: Renamed argument 'numBins' of MatNormalization to 'nbrOfBins'.

o HARMONIZATION: Now MatNormalization utilized the aroma setting 'ram', which replaced argument 'numChunks' which is now deprecated.

Version: 1.9.4 [2011-02-08]

o GENERALIZATION: Now it is possible to specify the range of fragment lengths to be considered when normalizing for PCR fragment-length effects. Lengths outside the range ar treated as missing values. See argument 'lengthRange' to FragmentLengthNormalization.

Version: 1.9.3 [2011-02-04]

BUG FIXES:

o as.character() for an empty AffymetrixCelSet would throw exception "Argument 'x' is of length 1 although the range ([0,0]) implies that is should be empty.", while trying to infer the chip type.

Version: 1.9.2 [2011-02-01]

o CLEANUP/GENERALIZATION: Now all system tests for the Mapping10K_Xba142 chip type use public data sets. Before some of them used a private data set.

Version: 1.9.1 [2011-02-01]

o GENERALIZATION: With aroma.core v1.9.3 it is now possible to display spatial image and write them as PNG files if the 'png' package is installed, alternatively to the EBImage package.

o ROBUSTNESS: Removed some remaining partial argument calls.

o CLEAN UP: Removed explicit dependencies on EBImage in the code. The dependencies are still there, but via wrapper methods of aroma.core.

Version: 1.9.0 [2011-01-10]

o No updates. Submitted to CRAN.

Version: 1.8.3 [2011-01-09]

o Added writeCdf() for AffyGenePDInfo, which replaces pdInfo2Cdf(). An auxillary CEL file is no longer needed to create a CDF from an PDInfo package. Moreover, contrary pdInfo2Cdf(), the generated CDF now gets a correct/formal Affymetrix chip type.

BUG FIXES:

o createMonocellCdf(..., verbose=FALSE) for AffymetrixCdfFile would still create verbose output.

Version: 1.8.2 [2010-12-04]

BUG FIXES:

o Local variable 'pdName' of pdInfo2Cdf() was used before it was defined, which gave an error. Thanks to Guido Hooiveld at the Wageningen University, Netherlands, for reporting this.

Version: 1.8.1 [2010-11-22]

o ROBUSTNESS: Now extractAffyBatch() for AffymetrixCelSet asserts that the sample names are unique, which affy::ReadAffy() requires. Moreover, the sample names are now the fullnames not just the names.

Version: 1.8.0 [2010-11-07]

o Committed to CRAN. No updates.

Version: 1.7.4 [2010-11-04]

o ROBUSTNESS: Bumping the required versions of the dependent package in order to make sure we are not affected by old bugs.

Version: 1.7.3 [2010-10-02]

o Now doGCRMA() automagically makes sure that the default CDF is used in the GcRmaBackgroundCorrection step, while use a custom CDF everywhere else if set. Added argument 'type' to doGCRMA() which is passed to GcRmaBackgroundCorrection().

o GENERALIZATION: Now GcRmaBackgroundCorrection(..., type="affinities") can process also chip types for which there are no MMs and for which non-specific probes are explicitly specified.

o GENERALIZATION: Now GcRmaBackgroundCorrection calculates gcRMA probe affinites based on Aroma Cell Sequence (ACS) annotation files. For backward compatibility, it turns to Affymetrix probe-tab files if an ACS file is not located.

o ROBUSTNESS: Added more validation of the arguments passed to the constructor of GcRmaBackgroundCorrection and its internal functions. Also added more verbose output during processing.

o CORRECTION: The DESCRIPTION file suggested a package version that did not exist.

Version: 1.7.2 [2010-09-06]

o ROBUSTNESS: Added extractAffyBatch() for ChipEffectSet that gives an informative error message explaining why it doesn't make sense to do so.

Version: 1.7.1 [2010-08-14]

o Added doGCRMA() for AffymetrixCelSet and data-set names. doGCRMA() runs in bounded memory and replicates the results of gcrma() in the gcrma package with great precision.

Version: 1.7.0 [2010-07-26]

o Committed to CRAN. No updates.

Version: 1.6.8 [2010-07-21]

o CLEAN UP: Now getAverageFile() for AffymetrixCelSet no longer writes debug information to ${Rcache}/aroma.affymetrix/idChecks/.

Version: 1.6.7 [2010-07-19]

o Now byPath(..., cdf) for ChipEffectSet will silently try to retrieve the the monocell CDF if argument 'cdf' is the main CDF. If it fails an error is thrown. This makes it possible to specify the main/regular CDF (or chip type), instead of the monocell CDF, when retrieve a chip-effect data set.

BUG FIXES:

o The above byPath(..., cdf) updated was necessary in order to be able to retrieve chip-effect data set byName() after the update of byName() for AffymetrixCelSet in the previous version.

Version: 1.6.6 [2010-07-02]

o Now AffymetrixCelSet$byName(..., chipType="GenomeWideSNP_6,Full") will work (before chiptypes with tags would give an error). This is now done by first locating the CDF for the chip type (with tags).

o Added doASCRMAv1() and doASCRMAv2() for convenient allele-specific doCRMAv1() and doCRMAv2() wrappers.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Dropped argument 'transforms' from getImage() for AffymetrixCdfFile.

Version: 1.6.5 [2010-06-16]

o Added doRMA() for AffymetrixCelSet and data-set names. doRMA() runs in bounded memory and replicates the results of fitPLM() in the affyPLM package with great precision.

Version: 1.6.4 [2010-06-07]

BUG FIXES:

o Added argument shift=+300 to doCRMAv1().

Version: 1.6.3 [2010-05-30]

o Now translateFullName() of AffymetrixProbeTabFile translates 'PROBE_STRAND' to 'targetStrandedness'.

Version: 1.6.2 [2010-05-26]

o Started to add scripts for downloading example data.

Version: 1.6.1 [2010-05-19]

o CORRECTION: doCRMAv1() did not shift +300 the signals before doing the probe-level summarization.

BUG FIXES:

o Fixed a bug in PdInfo2Cdf(). Thanks Kasper Daniel Hansen for the report.

Version: 1.6.0 [2010-05-14]

o Package submitted to CRAN.

SOFTWARE QUALITY:

o Package pass system and redundancy tests.

o Package pass R CMD check on R v2.11.0 and v2.12.0 devel.

Version: 1.5.9 [2010-05-13]

o SPEED UP: Now the constructor AllelicCrosstalkCalibration() is set to recognize the Cytogenetics_Array chip type. This avoids having to scan the CDF for unit types and check for SNPs, which is slow and not really wanted for a constructor function.

o ROBUSTNESS: Now fromDataFile() of ChipEffectFile and FirmaFile, as well as convertToUnique() of AffymetrixCelSet allocates/creates data files atomically. As elsewhere, this is done by first creating and writing to a temporary file, which when complete is then renamed. This lowers the risk of generating incomplete files.

SOFTWARE QUALITY:

o ROBUSTNESS: Added a redundancy test of CRMA "v1.5" for the Cytogenetics_Array chip type.

BUG FIXES:

o convertToUnique() for AffymetrixCelSet would not recognize Windows Shortcut links.

DEPRECATED AND DEFUNCT:

o CLEAN UP/DEPRECATED: AffymetrixCelSet$createBlankSet() was removed, because it has not been used anywhere since 2007.

Version: 1.5.8 [2010-05-09]

o Made justSNPRMA(..., normalizeSNPsOnly="auto") for AffymetrixCelSet the default.

o Now all findUnitsTodo() for data sets checks the data file that comes last in a lexicographic ordering. This is now consistent with how the summarization methods update the files. Before it used to be the one that is last in the data set.

o Now all updateUnits() for data sets updates the data files in lexicographic order.

o Now CrlmmModel(..., recalibrate=TRUE) is the default.

o Now justSNPRMA(..., returnESet=TRUE) for AffymetrixCelSet returns an AlleleSet due to updates in oligo v1.12.0.

o Added extractAlleleSet() to SnpChipEffectSet. Replaces extractSnpQSet(), because the SnpQSet class was dropped in oligo v1.12.0 and replaced by the AlleleSet class.

BUG FIXES:

o fit() of CrlmmModel would not work with oligo v1.12.0 and newer.

o getCallSet() and getCrlmmParametersSet() of CrlmmModel used non-existing verbose object 'log' instead of 'verbose'.

Version: 1.5.7 [2010-04-22]

o Added groupUnitsByDimension() to AffymetrixCdfFile.

SOFTWARE QUALITY:

o ROBUSTNESS: Added redundancy tests for doCRMAv2() and writeDataFrame().

BUG FIXES:

o doCRMAv1() for AffymetrixCelSet used undefined 'csN' internally instead of 'csC'.

Version: 1.5.6 [2010-04-15]

BUG FIXES:

o computeAffinities(..., verbose=FALSE) of AffymetrixCdfFile would give throw "Error in reset(pb) : object 'pb' not found". Thanks Stephen ? at Mnemosyne BioSciences, Finland, for this report.

Version: 1.5.5 [2010-04-07]

SOFTWARE QUALITY:

o ROBUSTNESS: Added a test script for gcRMA background correction on the MoEx-1_0-st-v1 chip type.

Version: 1.5.4 [2010-04-06]

o Added an internal version of doCRMAv1().

o Added argument 'plm' to existing doCRMAv2().

Version: 1.5.3 [2010-03-31]

o Updated getProbeSequenceData() for AffymetrixCdfFile to recognize more NetAffx probe-tab files, e.g. MoEx-1_0-st-v1.probe.tab.

o KNOWN ISSUES: getProbeSequenceData() for AffymetrixCdfFile requires that the unit names in the probe-tab file match the ones in the CDF. This may cause issues if custom CDFs with custom unit names are used. This is another reason why we should move away from probe-tab files and instead use aroma binary cell sequence files.

Version: 1.5.2 [2010-03-26]

o Added argument 'defValue' to createFrom() for AffymetrixCelFile so that one can specify the default value for cleared elements.

Version: 1.5.1 [2010-03-14]

BUG FIXES:

o allocateFromCdf() of AromaCellCpgFile, AromaCellPositionFile, and AromaCellMatchScoreFile would drop all but the first tag.

Version: 1.5.0 [2010-02-22]

o Submitted to CRAN. No changes since v1.4.9.

SOFTWARE QUALITY:

o Package passes all redundancy tests.

o Package passes R CMD check on R v2.10.1 patch and R v2.11.0 devel.

Version: 1.4.9 [2010-02-22]

o Added AromaCellCpgFile.

SOFTWARE QUALITY:

o Added test script for AromaCellCpgFile and AromaCellPostionFile.

BUG FIXES:

o The settings in 'aromaSettings' loaded by aroma.core was overridden by default settings of aroma.affymetrix, even if they already existed.

Version: 1.4.8 [2010-02-21]

o ROBUSTNESS: Now updateUnits() of ChipEffectSet updates the files in lexicographic order. Before there was a risk that this was not done if fullname translators are changing the lexicographic ordering.

o MEMORY OPTIMIZATION: Now updateUnits() of ChipEffectSet cleans out the temporary data object extracted for each chip-effect file written. It also calls the garbage collector after each file written.

o Added verbose output to updateUnits() of ProbeAffinityFile.

Version: 1.4.7 [2010-02-16]

o MEMORY OPTIMIZATION: Now process() of AllelicCrosstalkCalibration clears the in-memory cache when finished.

o MEMORY OPTIMIZATION: Now AbstractProbeSequenceNormalization classes cleans out more unneeded objects.

o MEMORY OPTIMIZATION: Now doCRMAv2() removes as much as possible.

BUG FIXES:

o readDataUnitChromosomePosition() of AffymetrixNetAffxCsvFile failed to map chromosome 'MT' to 25. This bug was introduced in aroma.affymetrix v1.0.7.

Version: 1.4.6 [2010-02-13]

o Added an internal version of doCRMAv2().

BUG FIXES:

o exportTotalAndFracB() of SnpChipEffectSet returned all arrays in the output data set directory and not only the ones part of the input data set.

Version: 1.4.5 [2010-02-10]

SOFTWARE QUALITY:

o Added redundancy test for calculating bias-corrected sex-chromosome copy numbers.

Version: 1.4.4 [2010-02-08]

o Added appendVarArgs(boxplot.stats) so that one can pass argument 'show.names' to bxp() via plotRle().

Version: 1.4.3 [2010-02-03]

SOFTWARE QUALITY:

o Package passes R CMD check and all redundancy tests.

Version: 1.4.2 [2010-02-02]

o Updated to work with R.filesets v0.7.4 and aroma.core v1.4.4.

Version: 1.4.1 [2010-01-06]

o Now all binary files allocated have default NA values. This is done by an update in aroma.core v1.4.1.

Version: 1.4.0 [2010-01-04]

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.10.1 and R v2.11.0 devel and all of its redundancy tests.

BUG FIXES:

o After loading aroma.affymetrix, findCdf() would give "Error in if (regexpr(pattern, chipType) != -1) { : argument is of length zero", because AffymetrixCdfFile$findByChipType(chipType=NULL) was not valid. Now the latter returns NULL without complaining.

Version: 1.3.6 [2010-01-02]

o Adopted to work with aroma.core v1.3.7 and R.filesets 0.7.0.

o ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.

o ROBUSTNESS: Now all index arguments are validated correctly using the new 'max' argument of Arguments$getIndices(). Before the case where "max == 0" was not handled correctly.

Version: 1.3.5 [2009-12-04]

BUG FIXES:

o The test for allowing ASCII CDFs or not in setCdf() of an AffymetrixCelSet was only applied if getOption(aromaSettings, "rules/allowAsciiCdfs") was TRUE (should be FALSE).

Version: 1.3.4 [2009-11-24]

o CLEAN UP: Removed packages GLAD, DNAcopy and HaarSeg from the list of suggested packages in DESCRIPTION.

o CLEAN UP: Move more method for 'profileCGH' objects to aroma.core.

Version: 1.3.3 [2009-11-19]

DEPRECATED AND DEFUNCT:

o CLEAN UP: Move all (generalized) ChromosomalModel, CopyNumberChromosomalModel, and CopyNumberSegmentationModel to aroma.core from here.

Version: 1.3.2 [2009-11-18]

o GENERALIZATION: Removed all dependencies on Affymetrix data types for ChromosomalModel, CopyNumberChromosomalModel, and CopyNumberSegmentationModel.

o Added internal getNumberOfFilesAveraged() to CnChipEffectFile.

o Added isAverageFile() for AffymetrixCelFile.

o Added CnChipEffectSetTuple extending ChipEffectSetTuple.

o Now getChromosomes() of ChromosomalModel utilized UGP files (only). DChip GenomeInformation files are no longer supported.

Version: 1.3.1 [2009-11-13]

o ROBUSTNESS: Now arguments 'ces' and 'ref' and CopyNumberChromosomalModel have to be CnChipEffectFile|Set, otherwise an exception is thrown. Before it was possible to pass a SnpChipEffectSet unnoticed, although only total CNs are modelled. Added a test to testScripts/robustness/ asserting this. Thanks Pierre Neuvial at UC Berkeley for this report.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Moved most of AromaUflFile to aroma.core (from aroma.affymetrix).

Version: 1.3.0 [2009-11-01]

o New public release.

o More recent dependencies on Bioconductor packages.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.10.0 and all redundancy tests.

Version: 1.2.3 [2009-10-26]

o Added getExtensionPattern() to those GenericDataFile classes that have "single" filename extension, e.g. *.cfh but not *.cdf.bin. The other will be incorporated when we have thoroughly gone through the impact of including those as well.

BUG FIXES:

o Fitting RlmPlm() would give an error reporting on a call to an internal preprocessCore function is incompatible. This occured with preprocessCore v1.7.1 or newer.

Version: 1.2.2 [2009-10-16]

o CLEAN UP: Cleaned up dependencies in DESCRIPTION.

Version: 1.2.1 [2009-10-02]

o Added argument 'onDuplicates' to importFromAffymetrixProbeTabFile() for AromaCellSequenceFile. If "error" ("warning"), an exception (warning) is generated whenever duplicated cell indices are detected in the probe tab file. If "ignore", they are ignored, which means that the last duplicated probe sequence will be what is finally imported.

o Added argument 'keepSequenceLengths' to importFromAffymetrixProbeTabFile() for AromaCellSequenceFile so that one can drop sequences of incorrect lengths, cf. HuGene-1_0-st-v1.probe.tab.

o Added getDefaultFullName() to AffymetrixFileSet and CnagCfhSet.

o CLEAN UP: Updated to use byPath() instead fromFiles().

BUG FIXES:

o Now getCdf() for AffymetrixProbeTabFile first searches for a CDF with filename .cdf, then ,.*.cdf.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed all getFullName() for all GenericDatFileSet classes.

Version: 1.2.0 [2009-09-09]

o New public release.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.9.2 and all redundancy tests.

BUG FIXES:

o Fixed broken/missing Rd links.

Version: 1.1.5 [2009-09-07]

DEPRECATED AND DEFUNCT:

o Renamed getUnitsOnChromosome() to getUnitsOnChromosomes() for the GenomeInformation class. The former now calls the latter for backward compatibility. This was done to make it more consistent with a similar method in aroma.core.

Version: 1.1.4 [2009-09-05]

o CLEAN UP: Removed the geneplotter package from Suggests:.

BUG FIXES:

o A few plot functions would generate "Error: 'smoothScatter' is not an exported object from 'namespace:geneplotter'". This would occur with geneplotter v1.21.5 or newer. This is because we called geneplotter::smoothScatter(), but that function was moved from geneplotter v1.21.4 to the graphics package of R v2.9.0. For backward compatibility, we now provide a patch (in aroma.core).

DEPRECATED AND DEFUNCT:

o CLEAN UP: Now static methods fromChipType() and fromName() of AffymetrixCelSet and other classes are defunct. Instead, use static methods byChipType() and byName() instead.

Version: 1.1.3 [2009-08-12]

o Now findByName() of AffymetrixCnChpSet, CnagCfhSet, and DChipDcpSet also utilize ditto of AffymetrixCelSet, because the code was identical to the latter.

o Now findByName() of AffymetrixCelSet calls ditto of GenericDataFileSet of the R.filesets packages, which means that Windows Shortcut links also in subdirectories are recognized.

Version: 1.1.2 [2009-07-08]

o Added getListOfUnitTypesFiles() to AffymetrixCelSetTuple, ArrayExplorer, and ChromosomalModel.

o Added getUnitTypesFile() for AffymetrixCdfFile, AffymetrixCel{File|Set}, AffymetrixCnChpFile, AffymetrixPlatform and TransformReport.

o Now AffymetrixCdfFile implements also the UnitTypesFile interface.

o ROBUSTNESS: Updated process() of AbstractProbeSequenceNormalization to write to a temporary file which is the renamed. This will lower the risk for generating corrupt files in case of interrupts.

Version: 1.1.1 [2009-06-30]

o Moved packages 'gcrma' and 'gsmoothr' from "Imports:" to "Suggests:", because the former class of packages is required by R CMD check, whereas the latter is not (via an option). This will allow the package to build and pass the checks on the CRAN servers.

BUG FIXES:

o Added missing getExpectedOutputFullnames() for MatSmoothing.

o ROBUSTNESS/BUG FIX: Now plot() of CopyNumberSegmentationModel asserts that the RColorBrewer package is available at the very beginning. This will avoid generating image files where the data points are missing.

Version: 1.1.0 [2009-05-29]

o New public release. No updates.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.9.0 and all redundancy tests.

Version: 1.0.8 [2009-05-27]

o SPEED UP: Now process() of MatSmoothing is several times faster due to code optimization and utilizing of the new 'gsmoothr' package.

o ROBUSTNESS: Updated process() of MatSmoothing to write first to a temporary file which is then renamed. This lower the risk for corrupt output files due to processing interrupts.

o ROBUSTNESS: Now the constructor of MatSmoothing does more tests of the validity of the 'design' matrix argument.

o Now the chip type validation of fromFiles() for AffymetrixCelSet is aware of tags in the chip type of the CEL files. This may happen if custom CDFs are used are their full chip types are stored in the CEL files, e.g. Hs_PromPR_v02,Harvard,ROIs,unique.

Version: 1.0.7 [2009-05-20]

o Now readDataUnitChromosomePosition() for AffymetrixNetAffxCsvFile also recognize 'M' for chromosome 25.

o GENERALIZATION: Updated fitCnProbes() of UnitModel to identify single-cell CN units, and ignore multi-cell CN units, which will be process like the other units. By not assuming single-cell CN units, this methods should also apply to other CDFs, e.g. the new Cytogenetics_Array.

o CLEAN UP: Moved the Explorer class and its support files under inst/ from aroma.affymetrixd to aroma.core.

o CLEAN UP: Moved the AromaCellPositionFile class from aroma.affymetrix to aroma.core. o EXCEPTION HANDLING: Methods that creates/modifies files will give a clear error message if the file permissions does not allow it.

o ROBUSTNESS: Now all arguments that are expected to be exactly one character string (not an empty vector or a vector of length two) are asserted to be that too. This closes some potential bugs.

o Package passes R CMD check on R v2.9.0.

BUG FIXES:

o getCdf() for AffymetrixProbeTabFile would fail if the CDF had no tags.

o fit() for CrlmmModel was calling oligo::getM(), but that method was later moved to oligoClasses. Now we just do getM().

DEPRECATED AND DEFUNCT:

o Removed obsolete patch of affxparser cdfMergeStrands().

Version: 1.0.6 [2009-05-16]

o CLEAN UP: Generalized CopyNumberSegmentationModel such that subclasses no longer have to implement fitOne(), but instead only getFitFunction(), which should return a segmentByNnn() function for the RawCopyNumbers class.

o CLEAN UP: Moved all drawCnLevels(), extractCopyNumberRegions() and extractRawCopyNumbers() [for DNAcopy, HaarSeg and profileCGH] to aroma.core v1.0.6 (will eventually end up in aroma.cn).

BUG FIXES:

o In the most recent version of oligo, its justSNPRMA() requires that oligo is loaded, i.e. oligo::justSNPRMA() will not work. Updated justSNPRMA() for character to require oligo.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed obsolete fitGlad() for CnChipEffect{File|Set}.

Version: 1.0.5 [2009-05-10]

o BETA: Updated several methods of the package to handle the new way getOutputDataSet() of AromaTransform scans and loads data sets. This new way is the first step towards supporting output directories that contains more data files than the input data set, which for instance can occur if the same data set is split up and processed in subsets. The new approach will also try to order the output files accordingly with the input files.

o Added readSequenceDataFrame() for AffymetrixProbeTabFile.

o Updated getFitUnitGroupFunction() of RmaPlm to work with the new oligo v1.7.19 as well.

o CLEAN UP: computeAffinities() of AffymetrixCdfFile loaded the 'matchprobes' package, but never used it.

o CLEAN UP: Now computeAffinities() of AffymetrixCdfFile uses the AffymetrixProbeTabFile class to read probe sequences.

o CLEAN UP: Now findByChipType() of AffymetrixProbeTabFile only search according to "modern" rules. The by now really old alternative search rules have been made deprecated, i.e. it still uses those but, if a file is found, it gives an error saying that the the method is outdated. This should not affect anyone these days, but just in case, it is included.

SOFTWARE QUALITY:

o Package passes redundancy tests.

o Package passes R CMD check on R v2.9.0.

Version: 1.0.4 [2009-04-16]

o BETA: Added NormExpBackgroundCorrection which does background correction according to the normal exponential model. It utilizes the limma package for this. The default settings give identical results as RmaBackgroundCorrection, which uses affy.

o Made several modifications to computeAffinities() for AffymetrixCdfFile which allows us to compute affinities also for PM-only chip types, e.g. Gene 1.0 ST arrays: (i) added a different stream for PM-only (with NCs), (ii) left the PM+MM array code mostly untouched, and (iii) fixed some assumptions about the columns of the probe_tab file.

BUG FIXES:

o The GcRmaBackgroundCorrection method would mix up PMs and MMs in the model estimation. This bug was introduced in aroma.affymetrix v0.3.4 (January 20, 2007). It was located to the internal bgAdjustGcrma() method.

Version: 1.0.3 [2009-03-22]

o BETA: Added GcContentNormalization2 which extends the generic AdditiveCovariateNormalization class.

o BETA: Added abstract AdditiveCovariateNormalization.

o BETA: Added AromaUnitGcContentFile and AromaUgcFile to hold GC contents.

Version: 1.0.2 [2009-02-22]

o Added getCdfBin() and getChipType() to DChipDcpSet.

o Added findByChipType() and byChipType() to DChipCdfBinFile. Added argument fullname=TRUE to getChipType() of DChipCdfBinFile.

o Added exportTotalCnRatioSet() to AffymetrixCnChpSet.

o Wherever argument 'ram' exists, it defaults to the value of a global settings. To change the default, do for instance setRam(aroma.affymetrix, 10).

o CLEAN UP: Removed the implementation of byChipType() for the AromaUnitTabularBinaryFile class that would scan annotationData/ for matching CDFs before deciding which file to use. That class should not depend on a specific platform. Now the implementation is solely in the aroma.core package.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed deprecated argument 'moreUnits' of fit() of ProbeLevelModel. Use argument 'ram' instead.

Version: 1.0.1 [2009-02-13]

o Added getAromaUnit{Total|FracB}CnFileSet() to SnpChipEffectSet, which uses protected exportTotalAndFracB() to SnpChipEffect{File|Set}.

o ROBUSTNESS: Added support for optional validation/selection by the number of units/cells to all static byChipType() methods. This is done by specifying argument nbrOfUnits/nbrOfCells.

o CLEAN UP: Suppressing warnings about "truncating string with embedded nul" in rawToChar() when using affxparser::readCcgHeader().

o CLEAN UP: Cleaned up the MatSmoothing class.

o CLEAN UP: Cleaned up the AffymetrixCelSetTuple class.

SOFTWARE QUALITY:

o Package pass R CMD check and all redundancy tests.

BUG FIXES:

o setMergeStrands() of SnpPlm and setCombineAlleles() of CnPlm did not update the setting of the PLM itself, only the settings of the underlying parameter files. SnpPlm itself, only only the underlying parameter files. Added getMergeStrands() to SnpPlm and getCombineAlleles() to CnPlm.

Version: 1.0.0 [2009-01-12]

o Added alpha version of the CrlmmModel (currently only for 100K & 500K).

o Added justSNPRMA() replicating ditto in the oligo package.

o Added alpha version of the HaarSegModel.

o Added plotAllelePairs() for AllelicCrosstalkCalibration.

o Added argument 'zooms' to the constructor of ChromosomeExplorer.

o Now process() of AlleleSummation returns immediately if already done.

o Added more methods and classes which eventually will allow analysis of Affymetrix tiling arrays.

o Added trial version of AromaCellPositionFile.

o Added extractCNT() and writeCNT() for SnpChipEffect{File|Set}, which exports CNT data files that can be imported by Affymetrix GTC Browser.

o Added argument 'units' to readDataFrame() to GenomeInformation.

o ROBUSTNESS: Now MultiArrayUnitModel:s assert that there are at least two arrays in the data set.

BUG FIXES:

o CLEAN UP: createFrom() for AffymetrixCelFile had verbose=TRUE as default.

o AlleleSummation would not work for chip types containing exclusively SNP units. It expected some non-SNP units.

o There was no extractTotalAndFreqB() for CnChipEffectSet, but only for CnChipEffecSet (misspelled). Thanks Pierre Neuvial for spotting this.

o Now process() avoids sets of pairs with too few probe pairs. This could happen because of the new getSetsOfProbes() working off the probe sequence files.

o getUnitIntensities() of AffymetrixCelSet would drop the array dimension if only one array was read. This caused for instance PLM fitting to given an error when only one array was included.

o Methods returning ChipEffectSet would not "update" the returned data set, which for instance had the effect of not updating/setting attributes for sample annotation files.

o Lines of code (excluding comments) using grep -v "#" *.R | wc -l: aroma.affymetrix + aroma.core: 43657+10510 = 54167.

Version: 0.9.6 [2008-12-04]

o Now CbsModel and GlabModel display any optional/additional arguments passed to the internal segmentation method in the verbose output.

o Added argument 'model' for AllelicCrosstalkCalibration to quickly specification of default parameter settings according to the CRMA and CRMA v2 model.

o Added argument 'pairBy' for AllelicCrosstalkCalibration to specify how the allele probe pairs are identified. Historically we inferred this from the CDF, but it is safer and more generic to do this from the probe sequences, which then requires an ACS annotation file.

o Now argument 'targetFunctions' of FragmentLengthNormalization can also be "zero", which then specifies a predefined constant target function.

o Added support for importing probe sequences from Affymetrix BPMAP files via the importFromBpMap() for AromaCellSequenceFile.

o Added classes and methods in preparation for supporting analysis of tiling arrays.

o Now fitCnProbes() of UnitModel only fits non-fitted CN units.

o SPEED UP: extractMatrix() of AffymetrixCel{File|Set} is now faster when argument 'cells' is specified.

o SPEED UP: Now BasePositionNormalization is 2-3 times faster due to memoization and a more clever prediction algorithm.

o MEMORY OPTIMIZATION: Added abstract normalization class LinearModelProbeSequenceNormalization that fits linear models based on probe sequences in bounded memory. This is done by building up the normal equations incrementally and then call solve(). It is the generation of normal equations that otherwise consume most of the memory. The BasePositionNormalization class now inherits from this memory-efficient class, which means we can now do probe-position normalization on GenomeWideSNP_6 arrays using less than 1GB of RAM.

o MEMORY OPTIMIZATION: Forgot to clean out weight estimates in ProbeLevelModel objects when cleaning out the memory cache.

BUG FIXES:

o For allele-specific estimates, FragmentLengthNormalization would correctly estimate normalization scale factors, but due to a typo, it effectively only update the signals for allele A. According to the source code repository, this has been a bug from the very beginning when allele-specific estimates was claimed to be supported.

o RmaPlm(..., flavor="oligo") was broken, because oligo was updated.

Version: 0.9.5 [2008-10-17]

o Package pass R CMD check on R v2.7.2 and R v2.8.0rc.

Version: 0.9.4.7 [2008-10-16]

o Added nbrOfCellsPerUnitGroup() and nbrOfCellsPerUnit() for AffymetrixCdfFile.

DEPRECATED AND DEFUNCT:

o Renamed getFitFunction() for all PLMs to getFitUnitGroupFunction(), because the latter is much more explanatory.

Version: 0.9.4.6 [2008-09-19]

BUG FIXES:

o process() of FragmentLengthNormalization did not return a data set for which the sample attributes has been updated according to optional sample annotation files (SAFs).

Version: 0.9.4.5 [2008-09-17]

o Added argument 'onMissing' to FragmentLengthNormalization, which is passed down to normalizeFragmentLength() [req aroma.light v1.9.2] to make it possible to normalize also units for which fragment lenghts are unknown. Previously such units were not normalized - for backward compatibility, onMissing="ignore" does exactly that.

o Now it is possible to specify enzyme names in argument 'enzymes' to readDataUnitFragmentLength() of AffymetrixNetAffxCsvFile.

o Added argument 'enzymesToUpdate' to importFromAffymetrixNetAffxCsvFile() of AromaUflFile in order to make it possible to specify both which enzymes to read and to update.

o ANNOTATION: Updated annotationData/genomes/Human,chromosomes.txt to contain data for the Mitochondrial genome ("chromosome") as well.

o CONSISTENCY: Now argument 'subset' of plotDensity() of AffymetrixCelFile and AffymetrixCelSet defaults to NULL (all probes). Before it was specifying the fraction 1/2 by default.

o DEPENDENCIES: Now aroma.affymetrix requires affxparser 1.13.8, because getUnitTypes() of AffymetrixCdfFile requires that version in order to correctly identify copy-number units.

o CLEANUP: Moved the handling of 'probeModel' and 'shift' to UnitModel from ProbeLevelModel.

BUG FIXES:

o TYPO: The error message for argument 'dataSet' in UnitModel() returned multiple strings, one per class.

Version: 0.9.4.3 [2008-08-30]

o Added options 'mergeStrands' and 'B' to AllelicCrosstalkCalibration.

BUG FIXES:

o Now the affy, affyPLM, and EBImage packages are forced to be after all of aroma.affymetrix, aroma.light, and R.huge on the search() path.

Version: 0.9.4.2 [2008-08-23]

o Moved the functions for reading dChip files to the new dChipIO package.

o Now readDataUnitChromosomePosition() of AffymetrixNetAffxCsvFile also recognizes chromosome "MT" (mitochondrial). It is encoded as Chr25.

o BETA: Added class AffymetrixCnChpSet.

Version: 0.9.4.1 [2008-08-19]

o Added argument 'arrays' to process() of ArrayExplorer so that it is possible to specify for which arrays images should be generated.

o Added support for specifying the type of target effects for any AbstractProbeSequenceNormalization method.

o ALPHA: Added argument 'flavor' to AllelicCrosstalkCalibration. However, fitGenotypeCone() of aroma.core has to be updated to recognize it.

o ALPHA: Added ReseqCrosstalkCalibration.

Version: 0.9.4 [2008-08-02]

o Public release.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.7.1 and R v2.8.0 devel on WinXP.

o Package passes all redundancy tests without errors.

Version: 0.9.3.5 [2008-07-31]

o UPDATE: Now computeAffinities() for AffymetrixCdfFile gives an error if there are no MMs in the CDF.

BUG FIXES:

o computeAffinities() for AffymetrixCdfFile searched for the probe-tab file using the chip type given by the fullname of the CDF and not the basic name.

Version: 0.9.3.4 [2008-07-30]

o Now getGenomeInformation() and getSnpInformation() reports the reason for why it thinks the located object is incompatible with the CDF.

o MEMORY OPTIMIZATION: Now argument 'ram' is passed down to getChipEffectSet() which in turn pass it down to getMonocellCdf(), which pass it to createMonocellCdf() in case the monocell CDF is missing. This increases the chances that fit(..., ram=) will work with small amount of RAM.

o MEMORY OPTIMIZATION: Now the validation part of createMonocellCdf() for AffymetrixCdfFile is also sensitive to the 'ram' argument.

Version: 0.9.3.3 [2008-07-22]

o MEMORY OPTIMIZATION: Pre-allocation of matrixes that start off with all NAs was always done by matrix(NA, ...), but since 'NA' has mode "logical" this would mean that non-logical matrixes would be coerced as soon as they were assigned as value. Updated all pre-allocation to be done as matrix(naValue, ...) where 'naValue' is of the correct storage mode.

o Now all findByName() assert that the data set name is not empty.

o CLEANUP: Removed allocateFromCdf() specific to AromaUgpFile since that is now implemented in a super class.

o ALPHA: Added BasePositionNormalization.

BUG FIXES:

o getAromaCellSequenceFile() of BaseCountNormalization would search using the full name of the chip type, e.g. GenomeWideSNP_6,Full.

o byChipType() of AromaUnitTabularBinaryFile failed to locate a valid tabular file if more than one was found and it was not the last one that was matching.

Version: 0.9.3.2 [2008-07-16]

o Now AffymetrixProbeTabFile inherits from TabularTextFile and "implements" AromaPlatformInterface. Previously it inherited from the AffymetrixFile class.

o Added extractMatrix() to AffymetrixCelFile for completeness.

o Added argument 'drop=FALSE' to all extractMatrix(), extractTheta(), and extractTotalAndFreqB().

o Added support for specifying the reference of any CopyNumberChromosomalModel as a single file (or a list of files if more than one set is used).

o MEMORY OPTIMIZATION: When calling extractRawCopyNumbers(obj) on an CopyNumberChromosomalModel object, the result would be cached in memory (in the object). This would result in an increasing memory usage when data was extracted from more and more arrays. The cache could be cleared by calling gc(obj), but avoid this problem by default, the method does no longer cache results. To cache, the method has to be called with argument 'cache=TRUE'. Thanks Jason Li for reporting this. o BETA: Added BaseCountNormalization.

o BETA: Updated FragmentLengthNormalization to handle allele-specific chip effect estimates as well.

o Lines of code (excluding comments) using grep -v "#" *.R | wc -l: aroma.affymetrix + aroma.core: 24902+8638=33540.

BUG FIXES:

o extractMatrix() of AffymetrixCelSet returned cells in a different than requested. Thanks Mark Robinson for reporting this.

o getChipType() of AffymetrixCelFile did not pass down '...' causing for instance getChipType(..., fullname=FALSE) to still return tags for ChipEffectFile:s.

o plm$treatNAsAs == "NA" for RmaPlm:s returned an incorrect number of probe affinities whenever missing values were exluded.

Version: 0.9.3 [2008-06-08]

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.7.0 patched. There are some warnings of broken links in the Rd pages though.

o Package passes all redundancy tests (processing time 17h 30min).

Version: 0.9.2.6 [2008-06-07]

o Update filename pattern for getOutputFiles() of Transform.

o Added missing getParameterSet() to ExonRmaPlm, so that 'mergeGroups' is also returned.

o BETA: Added setParallelSafe() to Explorer classes to make them (somewhat) resistant against race conditions occuring when you run them on the same data set in parallel.

BUG FIXES:

o readUnits() would throw 'Error in readCelUnits(pathnames, cdf = cdf, ...) : No CDF file for chip type found: GenomeWideSNP_6', if the CDF was set to GenomeWideSNP_6,Full.CDF and no GenomeWideSNP_6.cdf file was found. This was because readUnits() retrieve (x,y) information units, which requires affxparser::readCelUnits() to locate the CDF to infer the number of probe column in order to map (x,y) to cell indices. Now readUnits() get the cell indices directly using getCellIndices(). Thanks Yue Hu for noticing this problem.

o The validation of arguments 'ceList' and 'refList' to internal getRawCnData() of CopyNumberChromosomalModel was too conservative. This caused it to throw 'Exception: Argument 'ceList' contains a non- ChipEffectFile: NULL' whenever multiple ChipEffectSet:s were modelled and one of them did not have data for one sample. One of the redundancy tests for the 100K platform was updated to test for this scenario. Thanks to Lavinia Gordon for spotting this.

o If no reference sets has been specified, then getReferenceSetTuple() of CopyNumberChromosomalModel would return too few reference files if some arrays were misssing for certain chip types. Thanks to Lavinia Gordon for spotting this.

o updateOnLoadJS() of ArrayExplorer did not use the fullname chip type, cause an error in ArrayExplorer:s for tagged chip types. Thanks to Maria Traka at BBSRC in UK for spotting this.

Version: 0.9.2.5 [2008-05-28]

o Cleaned up a bit. Package now pass R CMD check.

Version: 0.9.2.4 [2008-05-25]

o All extracted RawCopyNumbers objects now also set the 'chromosome' field.

o Now Transform inherits from new generic aroma.core::AromaTransform.

Version: 0.9.2.3 [2008-05-21]

o CLEAN UP: Moved more classes and methods from aroma.affymetrix to aroma.core: RawCopyNumbers, CopyNumberRegions, CopyNumberOutliers. Moved attribute methods from AffymetrixCel{File|Set} to AromaMicroarrayDataSet. Moved stextNnn() methods from AffymetrixFile to AffymetrixMicroarrayDataSet. Created superclass AromaMicroarrayDataSetTuple of AffymetrixCelSetTuple. There is probably more that was moved to aroma.core that I forgot to mention here. Please see aroma.core NEWS as well.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.7.0 patched. There are some warnings of broken links in the Rd pages though.

o Package passes all redundancy tests.

Version: 0.9.2.2 [2008-05-16]

o Now NnnChipEffectSet parameters are by default set by the parameters of the first file.

o Added support for getFullNames(..., translate=TRUE) of AffymetrixCelSetTuple.

Version: 0.9.2.1 [2008-05-11]

o Added allocate() to AromaUgpFile.

Version: 0.9.2 [2008-05-10]

o MAJOR: Moved all methods and classes that are independent of platform (e.g. GenericDataFile) to a new package aroma.core.

o ALPHA: Inserted new classes AromaMicroarrayData{File|Set} and AromaChipTypeAnnotationFile into the class hierarchy.

SOFTWARE QUALITY:

o Package passes all redundancy tests (which takes approx 24 hours to run) on R v2.6.1 on Linux.

Version: 0.9.1.4 2008-05-09

o Added byName() to AffymetrixCdfFile, which is identical to byChipType().

o Added argument 'rows' to readDataFrame() for GenericTabularFile.

o SPEEDUP: The internal getUnitGroupNamesFromUgcMap() for AffymetrixCdfFile was painfully slow for large UGC maps. Instead of 10-15 days(!) for for GenomeWideSNP_6, it now takes 50 seconds. This speeds up extractDataFrame(..., addNames=TRUE) for ChipEffectSet:s substantially. Thanks Nicolas Stransky for reporting this.

o UPDATE: Updated readDataUnitFragmentLength() of AffymetrixNetAffxCsvFile to support the NetAffx r25 CSV files.

o UPDATE: Now generic attributes are handled by GenericDataFile.

o CONSISTENCY: Now the FirmaModel also has calculateResidualSet() just as ProbeLevelModel got it.

o CONSISTENCY: Renamed argument 'chromosome' of getUnitsAt() of AromaUgpFile to 'chromosomes'. This was done in order to make it consistent with getUnitsOnChromosome() of GenomeInformation. Thanks Tim Keighley at CSIRO for pointing this out.

o CLEAN UP: Package R.native is no longer suggested.

o CLEAN UP: Moved several methods to new package 'matrixStats' that is specialized and optimized for matrix operations.

o CLEAN UP: Moved normalizeQuantileSpline(), normalizeFragmentLength, plotXYCurve, and predict() for lowess to aroma.light v1.7.2.

o CLEAN UP: Removed "patches" for rowMedians() and as.() since they are now available in all R v2.6.x installations.

o CLEAN UP: Renamed all readData() methods that return a data.frame to readDataFrame().

o CLEAN UP: Now we're using construct foo(static, ...) instead of static$foo(...) internally.

o ALPHA: Added getImage() for AromaUnitTabularBinaryFile and AffymetrixCdfFile.

o ALPHA: Added writeColumnsToFiles() for GenericTabularFile.

o ALPHA: By using process(..., aliased=TRUE) for ChromosomeExplorer the names of generated PNG files are inferred from the aliased full names. This makes it possible to control the names of across multiple chip types without having to rename the files. Note, aliased=TRUE is currently only working to alias the tags, whereas any aliased name portions are still ignored.

BUG FIXES:

o readRawData() for AffymetrixCelFile did not handle a zero-length 'indices' argument; it was interpreted as NULL, i.e. read everything. This is actually a bug in affxparser.

o getUnitGroupCellMap() for ChipEffectFile, ResidualFile, WeightsFile, and FirmaFile, gave an error if argument 'units' had zero length (non-NULL).

o Now it is possible to pass argument 'paths' to byName() of AffymetrixCelSet, which in turn pass it to findByName().

o getChipType(..., fullname=FALSE) of AffymetrixCdfFile would return the chip type as the 'tags' attribute if there were no tags.

o The default drawExtraAnnotations() returned error <simpleError in UseMethod("estimateStandardDeviation"): no applicable method for "estimateStandardDeviation"> causing the sigma estimate as well as the chip type annotation for non-GladModels to be missing.

o readDataFrame() of AffymetrixProbeTabFile did not return the correct number of rows if there were missing cells, which there are.

o applyRows() and lines() of CopyNumberRegions did not handle cases with zero regions.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed obsolete getDescription() from AffymetrixFileSet.

o CLEAN UP: Removed obsolete getSibilings() from AffymetrixCelSet.

o CLEAN UP: Removed obsolete gcrmaSummary() and rmaSummary().

o DEFUNCT: All getCellMap() are now defunct; use getUnitGroupCellMap().

Version: 0.9.1 [2008-04-04]

o Now setCdf() also reports on the two incompatible chip types involved if trying to set a CDF that is not compatible with a CEL file.

o Added getMainCdf() for AffymetrixCdfFile for retrieving the "main" CDF given a monocell CDF.

o Now the standard deviation across all CNs in a chromosome is calculated using a robust first-order difference estimator, which will make the estimate much less affected by copy-number changes.

o BETA: Added estimateSds() to CopyNumberChromosomalModel for estimating the standard deviation of the raw CNs (log2-ratios) robustly and so that change points have minimal impact. This is done by using a first-order difference variance estimator. The reading of the data can definitely be made faster, but at least it works for now. Added redundancy tests for this based on the 10K and the 100K chip types.

o BETA: Added static method allocateFromCdf() for AffymetrixCelFile.

o BETA: Added readDataFrame() for AffymetrixCdfFile (SLOOOOW! but will be faster when the underlying function in 'affxparser' is updated).

o BETA: Added getUnitGroupCellChromosomePositionMap() to both AffymetrixCdfFile and ChipEffectFile.

o BETA: Added isUnitGroupCellMap().

o BETA: Added matrixBlockPolish().

BUG FIXES:

o BUG FIX: The ArrayExplorer would generate image files to a directory under reports//,/..., i.e. the tags where replicated. This is a bug introduced in the latest release. Thanks to

o BUG FIX: getTableOfArrays() of AffymetrixCelSetTuple returned the incorrect array indices for the 2nd chip type if different arrays in the two sets.

o BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least) some locale, e.g. 'C' (where 'A-z' works). The only way to specify the ASCII alphabet is to list all characters explicitly, which we now do in all methods of the package. See the r-devel thread "invalid regular expression '[a-Z]'" on 2008-03-05 for details.

o BUG FIX: extractMatrix(..., cells=NULL), the default, would throw 'Error in order(cells) : argument 1 is not a vector'.

o BUG FIX: getUnitIntensities() would not pass arguments '...', e.g. 'stratifyBy', to readUnits() for AffymetrixCdfFile. Thanks to Tim Keighley, CSIRO, Sydney, for reporting this.

o BUG FIX: Calling readUnits() of an AffymetrixCdfFile without specifying the 'units' argument gave an error. Thanks again Tim Keighley.

o BUG FIX: Calling readUnits(..., units=cdfUnits, stratifyBy=stratifyBy) twice with different 'stratifyBy' arguments and with a 'cdfUnits' list structure containing the identical set of unit names, would cause readUnits() to incorrectly return cached results from the previous call.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed the backward compatibility patch from 2007-01-10 that made fromDataFile() of ChipEffectFile to add missing tags. If anyone still has such old chip effect files lying around, they have to either add the tags manually or reanalyze the data if they want the fullnames of the chip effect files to match the fullnames raw data files.

Version: 0.9.0 [2008-02-29]

o UPDATE/ROBUSTNESS: Now AromaUnitTabularBinaryFile:s stores the chip type in the file footer. This allows us to identify the correct file gives a full chip type. Because of this update, old UFL and UGP files become incompatible with the class and new version have to be downloaded. The chip type can be queried by getChipType(). It is now also asserted that the number of units in the file match the number of units in the corresponding CDF.

o TIME OPTIMIZATION: Now RmaPlm and ExonRmaPlm turn to median polish if there are more than 500 cells and 6 arrays in the unit group. Option: aroma.affymetrix.settings$models$RmaPlm$medianPolishThreshold. Moreover, if the unit group is ridiculously large (5000 cells), the unit group is skipped and all returned estimates are NAs. Option: aroma.affymetrix.settings$models$RmaPlm$skipThreshold.

o TIME OPTIMIZATION: Now as.character() for AffymetrixCelSet reports time stamps only for data set with less than 500 arrays. Option: aroma.affymetrix.settingsoutput$timestampsThreshold.

o UPDATE: Annotation data directories starting with a period are no longer searched when looking for annotation data files.

o UPDATE: GcContentNormalization would only normalize SNP units but now also CN probes are normalized.

o UPDATE: Now a CnPlm with combineAlleles=TRUE also handles SNPs with six groups; they occur at least once in a custom SNP CDF.

o GENERALIZED: Now SNPs and CN probes are infered from the CDF unit type and no longer from the unit names.

o Added boxplotStats() to ChipEffectSet for calculating NUSE or RLE boxplot statistics (also on a subset of arrays).

o Added getUnitTypes() for AffymetrixCdfFile.

o Added extractMatrix() and extractDataFrame() to Parameter{File|Set}, i.e. subclasses ChipEffect{File|Set} and Firma{File|Set} got it too.

o Added published paper to citation("aroma.affymetrix").

o CLEANUP: Now byName() can be used everywhere fromName() can be used. Same for byChipType() and fromChipType().

o MEMORY OPTIMIZATION: Now importFromDChip() for CnChipEffectSet uses much less memory when infering the cell indices. o Updated importFromDChip() for CnChipEffectSet so that it imports data exported by more recent versions of dChip. In recent versions the standard-error columns are named '*SE' whereas before it were '*SD'. In either case, standard errors were exported (confirmed by author).

MAINLY FOR DEVELOPERS:

o CLEANUP: Renamed getMonoCell() to getMonocellCdf() and createMonoCell() to createMonocellCdf(), because the former had strange names.

o CLEANUP: Renamed usage of getCellMap() to getUnitGroupCellMap(). For backward compatibility, the old ones remain for a while.

o BETA: Added static importFromApt() for CnChipEffectSet.

o BETA: Added classes AffymetrixAptSummaryFile and AffymetrixCnChpFile.

o BETA: Added class AromaUfcFile.

o BETA: Added classes DChipChpFile and DChipChpSet.

o BETA: Added class AlleleSummation.

BUG FIXES:

o BUG FIX: The methods for calculating boxplot statistics did not handle "merged" CDF units correctly giving incorrect results.

o BUG FIX/ROBUSTNESS: It was possible to set a non-compatible CDF when using static fromFiles() of AffymetrixCelSet.

o BUG FIX: getTimestamp() for AffymetrixCelFile would return NA for Calvin files. Now they are also supported.

o BUG FIX: getCellIndices() of CnChipEffectFile would return an error if 'units==NULL'.

o BUG FIX: Since 'affy' defines standardGeneric("colnames") and S3 methods are not found by such S4 generic functions, we avoid that method name, and instead use getColumnNames().

Version: 0.8.3 [2007-12-18]

o UPDATE: Package patches installed by downloadPackagePatch() are now stored in ~/.Rpatches/ (previously in ./patches/). Thus, patches will be applied regardless of working directory.

o UPDATE: Changed fit() for FirmaModel to operate as fit() for ProbeLevelModel, where the units are read in in chunks and operated on over all chips, instead reading and operating chip-by-chip. Default summary is now the median residual instead of 1-UQR of weights. The added tags will reflect what settings are used.

o DEVEL: Added summaryOfUnits() for AromaUflFile.

BUG FIXES:

o BUG FIX: extractMatrix() of ChipEffectSet was broken (due to an internal bug in getCellMap() of ChipEffectFile).

o BUG FIX: When calling fit() on a ProbeLevelModel for chip type where no monocell CDF exists, an exception like "Could not create AffymetrixCdfFile object. No CDF file with that chip type found: GenomeWideSNP_6,Full,monocell" would be thrown. This is due to a bug introduced in previous version when trying to make sure custom CDFs are carried down more consistently. Now getMonoCell() of AffymetrixCdfFile will create the monocell CDF, if missing.

Version: 0.8.2 [2007-12-10]

o Added argument 'cdf' to static fromName() of AffymetrixCelSet. When using this argument, the 'chipType' argument is optional, and the returned CEL set will be using the specified CDF.

o In general, there is now better support for tagged CDFs. For instance, AffymetrixCdfFile$fromName("HuEx-1_0-st-v2", tags="core") can be used to locate 'HuEx-1_0-st-v2,core.CDF'.

o UPDATE: Now output sets of a FirmaModel are stored in firmaData/. Previously they were stored under modelFirmaModel/.

o UPDATE: Updated AffymetrixNetAffxCsvFile and AromaUflFile to better import fragment-length information from NetAffx files.

o ROBUSTNESS: Now getGenomeInformation() of AffymetrixCdfFile asserts that the located GenomeInformation annotation file is compatible with the CDF. Same for getSnpInformation(). Currently this can only be asserted for UGP & UFL annotation files.

o CONSISTENCY: Now getChipEffectSet() of ProbeLevelModel infers the monocell CDF from the CDF of the input data set and uses that when retrieving the chip-effect CEL set, not only when creating the set from scratch, but now also overriding the CDF according to the CEL header of existing sets. In other words, if the CDF is overridden for the input data set, it will also be overridden (with the corresponding monocell CDF) in the chip-effect set.

o CLEAN UP: Went through all classes where applicable and updated so that getTags() and getAsteriskTags() work properly. The latter was also renamed from getAsteriskTag() to getAsteriskTags() to indicate that it can actually return a multiple tags.

o CLEAN UP: Since much of the feature we used in 'affyPLM' moved to 'preprocessCore', packages 'affyPLM' (and 'affy') are no longer required by default. As with 'gcrma', the 'affy' package is only "suggested" and will be requested if need, e.g. when doing using one of background correction methods.

o DEVEL: Renamed all getAsteriskTag() methods to getAsteriskTags().

SOFTWARE QUALITY:

o Package pass R CMD CHECK on R v2.6.1 patch (WinXP).

o All testScripts/system/ scripts pass as well. Total processing time right of these scripts is ~18 hours.

BUG FIXES:

o BUG FIX: Tags from the input data set of FirmaModel were lost.

Version: 0.8.1 [2007-12-01]

o DEPENDENCIES: Package now requires R v2.6.0 or newer. The main reason for this is so we can move away from outdated package dependencies.

o NOTE: For AllelicCrosstalkCalibration and FragmentLengthNormalization, the default is now to exclude units/cells on sex chromosomes from the model fitting (in order not shrink XX and XY samples towards each other). For instance, AllelicCrosstalkCalibration argument 'subsetToAvg' defaults to '-XY' which automatically look up all units and then cells that are on ChrX and ChrY. For this to work, there must be a genome information file for the chip type. Note, '-XY' will work also on chip types for which there is no ChrY, e.g. Mapping250K_Nsp. The output data set will be get the extra tag '-XY' whenever this type of subsetting is used. To fit with all units, use 'subsetToAvg=NULL'.

o MODEL UPDATE: The AllelicCrosstalkCalibration method would, if 'targetAvg' was specified (default), rescale the probe signals such that the average of each allele-pair group would equal the target average (default =2200). However, this approach would make it hard to correct for other kinds of systematic effects, e.g. varying mixing proportions of target DNA from different enzymes. For instance, on the GenomeWideSNP_6 chip type the symptom could be that raw CN estimates for CN probes would be biased compared with SNP units. The default, for these SNP & CN chip types ("5.0" & "6.0") is now to rescale all signals on the array together, i.e. basically a median scale normalization. For the SNP only chip types ("10K", "100K" & "500K") the default is to rescale by group.

o UPDATE: Updated AffymetrixNetAffxCsvFile to recognize enzyme fragment annotation data for the new GenomeWideSNP_6 CSV files.

o CLEAN UP: Moved the following methods to R.utils: copyFile(), dataFrame(), isEof(), and reassignInPackage().

o CLEAN UP: normalizeAverage.{matrix,list}() is now instead in the aroma.light package.

SOFTWARE QUALITY:

o Package pass R CMD check on R v2.6.1 patched as well as all redundancy tests in testScripts/.

o TESTS: Added test script for HuEx-1_0-st-v2 by Elizabeth Purdom.

BUG FIXES:

o BUG FIX: The multi-enzyme model implemented was not the one in mind; The correction for the multi-enzyme data points was not right. The example(normalizeFragmentLength) has been updated to also display the normalized log-ratios (as a function of fragment length as well as they densities). That revealed the bug. The example also tests the case for non-aliquot mixing proportions between enzymes. This is indeed "automagically" corrected for by the model itself, i.e. there is no need to estimate the mixing proportions explicitly.

o BUG FIX: The AllelicCrosstalkCalibration introduced in previous version was broken for 10K (and possibly also for 100K and 500K).

Version: 0.8.0 [2007-11-25]

o Updated FragmentLengthNormalization to normalize data for which more than one enzyme was used to digest the DNA. See class for model constraints and assumptions. Tested on GenomeWideSNP_6 data.

o Now argument 'chromosome' for getUnitsOnChromosome() needs to be specified explictly. Before its default was '23'.

o Now the asterisk tags ('*') of the ProbeLevelModels are no longer interpreted in the constructor, but by getTags() in the Model class.

o MEMORY OPTIMIZATION: getCellMap() and getCellIndices() for ChipEffectFile et al. now extracts data in chunks.

o BETA: Added low-level methods fitWHRCModel() and fitWHLAPLM().

Version: 0.7.2 [2007-09-30]

o Now the main HTML file for ChromosomeExplorer is ChromosomeExplorer.html, which is in analogue to how the ArrayExplorer works. This HTML now loads to a different Javascript file with a different name so that already existing index.html ChromosomeExplorer files will still work.

o By default, all CopyNumberSegmentationModel plots do now display non-robust and robust estimates of the standard deviation of the raw CNs across the complete genome. Note that this is not done segment by segment, so if there are alot of aberrations then these estimates will be biased.

o ROBUSTNESS: Now getAverageFile() of AffymetrixCelSet detects if an average file has been deleted between calls and recalculates it, if missing.

o BETA: Did some "behind the scenes" restructuring of the CopyNumberSegmentationModel by adding an even simpler superclass ChromosomalModel, allowing for simpler types of modelling along the chromosomes.

SOFTWARE QUALITY:

o Package pass R CMD check on R v2.6.0 beta and all of the redundancy tests. The redundancy tests are now available under testScripts/ in the package directory.

BUG FIXES:

o BUG FIX: Forgot to update ExonRmaPlm to handle compatibility issues with affyPLM/preprocessCore. See below.

o BUG FIX: The CopyNumberSegmentationModel:s did not support paired copy-number analysis by specifying references files explictly. To do this, pass an additional list of CnChipEffectSet:s via constructor argument 'refTuple'. This list my contain the same chip types, and each chip type must contain exactly the same number of files. Note, the hashcode-generated hexadecimal tag added to the save CopyNumberSegmentationModel results, but also as part of the ChromosomeExplorer image files, will be different in this new version, meaning the package will not detect already existing segmentation estimates. You can always one run chromosome, check the new hashcode, and rename existing files to have the same one.

o BUG FIX: Before duplicated tags were removed using unique(), but that would also remove duplicated tags that were not "neighbors", e.g. the 2nd "-X" tags in "ACC,-X,RMA,A+B,FLN,-X" was removed. Now only duplicated neighboring tags are removed, e.g. "-X,-X,-X".

DEPRECATED AND DEFUNCT:

o CLEAN UP: Moved several classes to aroma.affymetrix.extras that are haven't been updated in a long time and are likely to be broken. This was done in order make this package easier to maintain. If this broke something for you, please contact me.

Version: 0.7.1 [2007-09-18]

o Now fit() of CopyNumberSegmentationModel reports timing information for each chromosome fitted when in verbose mode.

o Now importFromAffymetrixNetAffxCsvFile() of AromaUgpFile averages positions if multiple positions were available for a particular unit.

o ROBUSTNESS: Made createFrom() of AffymetrixCelFile fail safe, that is, the destination file will not be created unless it is complete. This is done by first create/writing to a temporary file which is then renamed at the end. This should minimize the risk of creating incomplete CEL files.

o ROBUSTNESS: Added internal fileCopy() which copies a file via a temporary file which is renamed. All file copying in the package is now done via this method.

o BETA: Added trial version of ScaleNormalization.

o BUG FIX: Due to a migration of code from affyPLM to preprocessCore, the fit function returned by getFitFunction() would not work with affyPLM >= 1.13.9. Now getFitFunction() adopts to the version of affyPLM/preprocessCore installed. If preprocessCore v0.99.16 or newer is available, that is used, otherwise affyPLM v1.13.8 or older is used. This has been veried to work on i) R v2.5.1pat with affyPLM v1.12.0, and R v2.6.0alpha with preprocessCode v0.99.16. (affyPLM v1.13.6).

BUG FIXES:

o BUG FIX: The workaround storing single-probe sdTheta estimates as a small value was set for single-chip not probe cases.

o BUG FIX: getFragmentLengths() of UflSnpInformation would thrown an error "Unknown fields: fragmentLength". Now getDataColumns() returns the correct names.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Removed obsolete copyFile() from AffymetrixFile in favor of copyTo() in GenericDataFile.

Version: 0.7.0 [2007-09-15]

o Now it is possible to specify the genome used for segmentation and plotting. This can be done either via argument 'genome' in the constructor or by setGenome() of CopyNumberSegmentationModel. A corresponding (,)*,chromosomes.txt file should be put in annotationData/genomes//. If not found there, the file is searched for in the annotationData/ directory installed with the package. If the file is not found, setGenome() will give an error. If not specified, the genome defaults to "Human". The above file specifies the number of bases per chromosome, which is used when plotting chromosomal data. The previous file 'hgChromosomes.txt' is now deprecated and obsolete.

o Now CopyNumberSegmentationModel only adds cytobands to genomes for which cytoband information is available. Currently this is hardwired only the "Human" genome. For all other genomes, there will be no cytoband.

o Now AllelicCrosstalkCalibration corrects also non-SNP PM cells by substracting a global offset and rescaling towards target average. The global offset is calculated as the weighted average of all allelic offsets. SNP probes are calibrated in the same way as before.

o Updated all places with SNP regular expression "^SNP" to "SNP_" in order to also match units named "AFFX-SNP_...".

o SPEED UP: Now getCellMap() of ChipEffectFile caches (large) results to file.

o SPEED UP: Now getOutputDataSet() of FragmentLengthNormalization set and pass down 'mergeStrands' and 'combineAlleles' to ditto of the super class, if applicable. This way we avoid having to infer those arguments from the contents of the files. This gives an significant speed up for large chip types.

o ROBUSTNESS: Now the RmaPlm fit function detects cases where a probe get zero weight for all arrays. In such (rare) cases, parameter estimates equals NAs. Before an LAPACK error was thrown.

o ROBUSTNESS: Added validate that the 'name' of an AffymetrixCelSet and AffymetrixCelFile is of at least length one.

o ROBUSTNESS: Now isDone() of Transform throws an error if too many output files are found. Before it used to return FALSE.

o WORKAROUND: If there is only one probe, then fit function of AvgPlm would return theta=y:s, and sdTheta=0:s. However, when searching for units to do, we test (sdTheta <= 0). The workaround is to store the smallest float available instead of zero.

o BETA: Added GenericDataFile, GenericDataFileSet, and GenericTabularFile.

o BETA: Added AffymetrixTabularFile, AffymetrixNetAffxCsvFile, AromaUgpFile, and AromaUflFile.

o BETA: Added UflSnpInformation and UgpGenomeInformation interfacing to UGP and UFL files.

o BETA: Added AvgPlm, AvgSnpPlm, AvgCnPlm.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.5.1pat & R v2.6.0alpha on Windows XP. It also passes all redundancy tests on Linux.

BUG FIXES:

o BUG FIX: Now more effort is made to ensure that all CEL files are generated with an upper-case filename extension (.CEL) and not (.cel). Thanks Jeremy Silver for reporting problems on this.

Version: 0.6.2 [2007-09-07]

o Now setCdf() of AffymetrixCelSet throws an (informative) error message whenever one tries to use an ASCII CDF file. This behavior can be changed by setting rule 'aroma.affymetrix.settings$rules$allowAsciiCdfs' to TRUE in the options. The reason is that working with ASCII CDF files is extremely slow and memory inefficient. Use affxparser::convertCdf() to convert a CDF into a binary format.

o Updated AllelicCrosstalkCalibration internally. It now also stores the model parameter estimates to file (using a plain save() file format).

o MEMORY OPTIMIZATION: Instead of doing unlist(getCellIndices(cdf, ...), use.names=FALSE), we can now do getCellIndices(cdf, useNames=FALSE, unlist=TRUE), which is much more memory efficient, e.g. for the GenomeWideSNP_6 chip the former uses 25x more memory, which means that instead of using 1.4GB we can get away with 60MB.

o CLEAN UP: All calibrateAllelicCrosstalk() methods are now removed. Use the AllelicCrosstalkCalibration class instead.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.5.1 and R v2.6.0 devel on Windows. All redundancy tests works on Linux.

Version: 0.6.1 [2007-09-05]

o Added support for fitting copy-number regions using the (fast) Circular Binary Segmentation (CBS) method of Venkatraman et al. (2007). The method is implemented by the new CbsModel class. Consider this class to be very much in a beta version.

o Added super class CopyNumberSegmentationModel, which provides most of the framework to fit and plot segmentation models. By subclassing this class, new segmentation methods can be added. Current subclasses are GladModel and CbsModel. ChromosomeExplorer was updated to handle multiple segmentation methods.

o Now the startup message when loading the package is generated with packageStartupMessage() so that it can be suppressed.

o Put more effort in generating more consistent hash codes that becomes part of the filenames of the averaged files. This modification is likely to lead to new hashcodes, and there for new filenames such that aroma.affymetrix will not detect existing "average" files. In turn, this will mean that stored results from GladModel will not be recognized (unless you rename files with the new hashcodes).

o Added a "patch" to make sure that there is rowMedians() supporting missing values by looking for the correct version of Biobase, R.native or just an apply() notes. This does unfortunately mean that generated hashcodes my be different so certain average CEL files will be recalculated, and in turn segmentation results will be regenerated.

o PACKAGE DEPENDENCIES: Made R.native an "Supports" package, since it is only used for rowMedians() in case the right Biobase version is not availble. R.native is now optional.

BUG FIXES:

o BUG FIX: getAverageFile() of AffymetrixCelSet had 'na.rm=FALSE' by default, which caused a lot of missing values in the average. In turn, this cause for instance raw CNs to become missing values.

o BUG FIX: When calling process() on a GcRmaBackgroundCorrection, an exception would be thrown with "bgAdjustGcrma() is deprecated. Please use the GcRmaBackgroundCorrection class". The same happend with OpticalBackgroundCorrection. This was due to a typo introduced in v0.5.3 when making the underlying functions deprecated. Thanks Jeremy Silver for troubleshooting and reporting this.

DEPRECATED AND DEFUNCT:

o CLEAN UP: Deleted obsolete /inst/chromosomeExplorer/ from source.

o CLEAN UP: Removed some obsolete affxparser patches.

Version: 0.6.0 [2007-08-17]

o Steps have been taken to support working with Calvin CEL files. This is still in testing, but from first tests it looks like it is working.

o Now calculateResidualSet() of ProbeLevelModel only loads probe-affinity estimates if needed, i.e. if residuals are already calculated this function will return faster now.

o Now createFrom(..., methods="create", clear=FALSE) of AffymetrixCelFile will first create an empty file, and then copy all CEL data to the new file. This way createFrom(..., methods="create", clear=FALSE) and createFrom(..., methods="copy", clear=FALSE) should give CEL files containing the same data. createFrom() also accepts a vector of options in 'methods' (renamed from 'method') which will be tried in order until success.

o Now getImage() of AffymetrixCelFile defaults to no interleaving, i.e. argument defaults to interleaved="none". The reason for this is that the previous default "auto" did not work too well and sometimes turned on interleaving although not needed. So, now one has to use interleaved="auto" ("v" or "h") when for instance getting images for spatial PLM residuals where an PM-only fit was done to a chip with MMs (otherwise every 2nd line will be blank). This also affects the ArrayExplorer; you pass the 'interleaved' argument via the process() call.

o Added support for dChip's 'snp6.0 genome info hg18.txt' file. Note, this only contains informations for SNPs, not CN probes.

o MEMORY OPTIMIZATION: calculateResidualSet() of ProbeLevelModel does part of the work in chunks.

o MEMORY OPTIMIZATION: Made getCellIndices() of AffymetrixCdfFile more memory effiencent by reading and transforming data in chunks.

o MEMORY OPTIMIZATION: Made findUnitsTodo() of ChipEffectFile scan for units in chunks. This would bring done memory usage to about 5% of what is used to consume.

o MEMORY OPTIMIZATION: Now getAlleleProbePairs() of AffymetrixCdfFile processes the CDF in chunks in order to save memory. Before, processing the GenomeWideSNP_6.CDF would consume 1.5-2.0GB RAM, but now it is using less than 500MB.

o MEMORY OPTIMIZATION: ArrayExplorer now garbage collects after each image written. That save a few hundred MB.

o CLEAN UP: Removed findUnitsTodo() from ExonChipEffectFile, because it gave the same result as the one in super class ChipEffectFile.

SOFTWARE QUALITY:

o Package passes R CMD check on R v2.5.1 and R v2.6.0 devel.

o Package passes all redundancy tests.

BUG FIXES:

o BUG FIX: Removed internal trial encoding function added by mistake to the previous version.

Version: 0.5.6 [2007-08-10]

o Package passes R CMD check on R v2.5.1 and R v2.6.0 devel.

o AffymetrixFileSet class defines lapply(), which causes lapply() to redefined as a generic function, which in turn gives some overhead to "standard" lapply() calls due to method dispatching. All standard lapply() calls are now called as base::lapply(). Benchmarking: This changes makes fit() on SNP 10K roughly 10% faster.

o Now all generated CEL files are written with upper-case filename extension (.CEL). The main reason for this is that some other software don't recognize CEL files with lower-case extension (.cel). Existing CEL files that are in lower case (.cel) and that are generated by the package are renamed to upper case (.CEL). Same thing for generated CDF files.

BUG FIXES:

o BUG FIX: ArrayExplorer assumed identical sample names and color maps across chip types and plots. Now the set of samples and color maps displayed are unique for each chip type.

Version: 0.5.5 [2007-08-03]

o MISC: Keeping the normalizeAverage() that was moved to aroma.light, so that the the package works with aroma.light v1.4.x that comes with the BioC release. This means that it is only 'aroma.affymetrix', 'aroma.apd', and (optional) 'R.native' that are not on CRAN/BioC.

o This version was used at the BioC2007 practical.

Version: 0.5.4 [2007-08-02]

o Renamed static fromName() of AffymetrixCelSet to byName().

o Renamed fromChipType() of AffymetrixCdfFile to byChipType().

o Some of the dependencies were to weak in the DESCRIPTION file. Added explicit version dependencies also for Suggests and Imports packages.

BUG FIXES:

o BUG FIX: getCellMap() of ChipEffectFile would give an error if verbose output was on.

Version: 0.5.3 [2007-07-13]

o Now more verbose output is generated when a monocell CDF is created in the background.

o Added getFileFormat() to AffymetrixCdfFile and AffymetrixCelFile. These are also reported by the corresponding print() method.

o Made bgAdjustOptical(), bgAdjustRma(), and bgAdjustGcRma() deprecated. If used, an error will be thrown. Use the Optical-, Rma-, and GcRmaBackgroundCorrection classes instead.

o MEMORY OPTIMIZATION: Includes a patch to affxparser:::.initializeCdf() to make it much more memory efficient, e.g. when writing the CDF header unit names, it could consume >1.5GB RAM, whereas now it is in the order of 100-200MB. This patch will go away as soon as the affxparser package incorporates it.

o MEMORY OPTIMIZATION: Includes a patch to base::matrix() that does not create an extra copy when assigned a new value to a cell, e.g. the 2nd statement in the following would force a new copy of the matrix: x <- matrix(0, 5000,5000); x[1,1] <- 1; Thanks to Luke Tierney for troubleshooting and suggesting a patch; there are no immediate plans to include this patch in 'base' though.

SOFTWARE QUALITY:

o Package passes R CMD check on Rv2.5.1 (and R v2.6.0 devel).

o Package passes all (#1 and #2) redundancy test sets available on the group page. This was confirmed on R v2.5.1 on WinXP (1.5GB RAM).

BUG FIXES:

o BUG FIX: Now (private) createMonoCell() of AffymetrixCdfFile will build the monocell CDF to a temporary filename, and only when it is done, rename it to the final *,monocell.cdf filename. This will lower the risk for creating an invalid CDF, which for instance can happen if we run out of memory. Reading invalid CDFs will core dump R due to the affxparser and the Fusion SDK package.

o BUG FIX: The memory usage of fit() of the FirmaModel would increase linearly with the number of arrays processed. This was because read results where cached for each of the FirmaFile:s. Thanks Mark Robinson for reporting on this.

o BUG FIX: getOutputDataSet() of Transform would give "Error in fromFiles.AffymetrixCelSet(static, path = path, pattern = pattern,: formal argument "checkChipType" matched by multiple actual arguments". This was due to the recent adding of 'checkChipType=FALSE'. Fixed by adding 'checkChipType=FALSE' to fromFiles() of ChipEffectSet. Thanks Jeremy Silver at WEHI for report and troubleshooting this.

Version: 0.5.2 [2007-06-25]

BUG FIXES:

o BUG FIX: When getOutputDataSet() retrieved the output data set, the chip type of the CEL files would be validated against the path name, also when then CDF of the input set was overriden. Now the output data set is setup using 'checkChipType=FALSE'. Thanks Mark Robinson for troubleshooting this.

Version: 0.5.1 [2007-06-12]

o Moved normalizeAverage() to aroma.light.

o Replaced all require() with require("").

SOFTWARE QUALITY:

o Package passes R CMD check on Rv2.6.0 devel. This new version of R CMD check does a lot more validation on the code and several potential problems were found this way.

BUG FIXES:

o BUG FIX: When argument 'transforms' to getImage() of AffymetrixCelFile wasn't a list, then "Error: argument "transform" is missing, with no default" was thrown. Thanks Karen Vranizan, UC Berkeley for reporting this problem.

o BUG FIX: If an Affymetrix probe tab file is not found for the chip type, computeAffinitities() of AffymetrixCdfFile would throw "Error in paste(..., sep = sep, collapse = collapse): object "pattern" not found" instead of an intended and more information error.

o BUG FIX: getSiblings() for AffymetrixCelSet was broken.

o BUG FIX: Called getFile(ces, ...) instead of getFile(this, ...) in fitGlad() of CnChipEffectSet. If the GladModel was used to fit the GLAD model this bug has not affected the modelling.

o BUG FIX: Used getFileName() instead of getFilename() in exportToAPT() of SnpChipEffectSet.

Version: 0.5.0 [2007-05-10]

o getProbeAffinityFile() of ExonRmaPlm did not return the correct subclass.

o Added default zoom levels to updateSamplesFile() for ChromosomeExplorer. This is applies the first time process() is called.

o Removed dependency of the R.image package by removing writeSpatial() for the AffymetrixCelFile class. Use writeImage() instead.

o Now patchPackage(..., deleteOld=TRUE) removes not only old patches, but also patches that are older than the package itself. Thus, when loading the package, all old patches are automatically removed.

o Added argument 'apply=TRUE' to downloadPackagePatch() so that downloaded patches are applied immediately after being downloaded.

SOFTWARE QUALITY:

o Package passes R CMD check on Rv2.5.0 (and R v2.4.1).

o Package pass redundancy tests on R v2.5.0 (and R v2.4.1). This was confirmed to work on Windows XP.

BUG FIXES:

o BUG FIX: calibrateAllelicCrosstalk() for AffymetrixCelFile would output filenames containing only the name but not the tags.

o BUG FIX: If no valid timestamp was identified in the CEL header by getTimestamp() of AffymetrixCelFile, then as.character() would give "Error in sprintf(fmt, ...) : zero-length argument". Now it returns NA instead as a fall back if no valid timestamp is found. Thanks Mark Robinson, WEHI, for reporting this.

o BUG FIX: getRegions() and getLog2Ratios() of GladModel would give an error if only a subset of the chromosomes where queried.

Version: 0.4.9 [2007-04-22]

o BUG FIX: Added missing getExclCells() to QuantileNormalization. Thanks Elizabeth Purdom for the report.

Version: 0.4.8 [2007-04-19]

o Now non-positive signals are given weight zero when being fitted in the IWLS algorithm for the log-additive model of RmaPlm. This requires affyPLM v1.11.14. Thanks Ben Bolstad for adding support for weights.

o BUG FIX: getChipEffectSet() and getProbeAffinityFile() of the ExonRmaPlm class did not set the 'mergeStrands' parameter. Thanks Elizabeth Purdom for the fix.

Version: 0.4.7 [2007-04-12]

BUG FIXES:

o BUG FIX: fromFiles() of AffymetrixCelSet would give error "Exception: Pathname not found: annotationData/samples" if that directory was missing. Now it is instead created.

o BUG FIX: readData() of SampleAnnotationFile would open a text connection without closing it. This would eventually given an error about too many open connections.

o BUG FIX: There was a if (TRUE) {} statement in calculateResidualSet() that was supposed to be if (!fource) {} in the release version.

o BUG FIX: fromDataFile() of ResidualFile returned an AffymetrixCelFile but not a ResidualFile. This caused getResidualSet() of ProbeLevelModel to return a ResidualSet containing AffymetrixCelFile:s. The same bug was found for the WeightFile class.

Version: 0.4.6 [2007-04-04]

o Now fromFiles() in AffymetrixCelSet verifies that the CDF being assigned to the data set is compatible with the CEL files, i.e. have the same number of cells. The default is to infer the chip type from the name of the parent directory of the CEL files, but if that chip type is not compatible the chip type according to the the first CEL file will be used for the set.

BUG FIXES:

o BUG FIX: Loading aroma.affymetrix v0.4.5 (and v0.4.4?) on Windows would give: "Error in digest::digest(..., skip = skip, ascii = ascii) : unused argument(s) (skip = "auto", ascii = FALSE)".

o BUG FIX: Static fromFiles() in ChipEffectSet did not call ditto in super class AffymetrixCelSet but instead the one in grand-parent super class AffymetrixFileSet.

Version: 0.4.5 [2007-04-03]

o Now AllelicCrosstalkCalibration rescales by default allele A and allele B signals such that the get the same averages.

o Added ETA to verbose output of fit() for the ProbeLevelModel.

WORK IN PROGRESS (no guarantees):

o Now RmaPlm:s can handle non-positive signals either by setting the to a small number or to ignore them when fitting the PLM. See code of fit function(s) for more details.

o Added AffymetrixTsvFile to read the CNAT v4 "covariate" files.

o Added GcContentNormalization.

BUG FIXES:

o BUG FIX: Probe-affinities were not save, resulting in all zeroes. This was due to renaming getProbeAffinites() to getProbeAffinityFile().

o BUG FIX: ChipEffectGroupMerge would catch warnings (like errors) when create output CEL files, e.g. when getRelativePath() gave an unimportant warning.

o BUG FIX: getFitUnitFunction() for CnPlm was broken for PM-MM probe models for single group units, e.g. AFFX units, resulting in an error "Argument 'y' must have two dimensions: 3".

o BUG FIX: getFitUnitFunction() of CnPlm did not handle probe model "min1(pm-mm)".

Version: 0.4.4 [2007-03-26]

o Added BackgroundCorrection classes RmaBackgroundCorrection, GcRmaBackgroundCorrection, and OpticalBackgroundCorrection. These replaces methods bgAdjustRma(), bgAdjustRcRma(), and bgAdjustOptical() which are now deprecated.

o The ArrayExplorer class now handles multiple chip types.

o Now inferParameters() of the ChipEffectSet classes is looking at the 'intensity' (==theta) field instead of 'stdvs'. The reason for this is that 'stdvs' might be all zeros, e.g. after a fragment-length normalization.

WORK IN PROGRESS (no guarantees):

o Added AffymetrixCelSetTuple.

o Added the SpatialReporter class.

o Added the abstract Explorer class.

o Added calculateBaseline() to ChipEffectSet.

o Replaced all occurances of affxparser::copyCel() with createFrom() in AffymetrixCelFile.

o Lines of code (excluding comments): grep -v "#" *.R | wc -l => 24902

BUG FIXES:

o BUG FIX: clearCache() of AffymetrixCelSet did not clear the .readUnitsCache field.

Version: 0.4.3 [2007-03-15]

o Updated the GladModel to only work with chromosome indices (integers).

o Now the GladModel infers the set of possible chromosomes from the GenomeInformation file. This means it handles other genomes than the human genome better.

o Updated GenomeInformation to return chromosomes as indices and never with 'X' and 'Y' regardless of source. This is part of a moving the package to handle chromosomes as indices so that it will work with any genome not just the human.

o Fixed fit() for FirmaModel so that it checks array-by-array whether units have been fitted.

o Names of cache files are now made more consistent between R versions (and platforms) resulting in more cache hits and therefore faster processing.

o Now the package tries to keep the search path of packages in such an order that any package known to cause problems to aroma.affymetrix if loaded after aroma.affymetrix, will be inserted behind aroma.affymetrix in the search path. For example, loading the EBImage package after aroma.affymetrix used to cause complaints when calling display() on an ArrayExplorer.

o MEMORY OPTIMIZATION: Further optimized memory usage in: calculateResiduals() of ProbeLevelModel.

o Lines of code: grep -v "#" *.R | wc -l => 24106

WORK IN PROGRESS (no guarantees):

o Added getUnitGroupCellMap() to AffymetrixCdfFile.

o Added code for in-memory attributes to AffymetrixFile object. Certain filename tags are interpreted as attributes which are set when the AffymetrixFile object is instantiated. Note: Attributes are not carried over in transforms etc.

o Added the AromaGenomePositionFile class and subclasses AromaUgpFile and AromaCgpFile.

o Added extractMatrix() for ChipEffectSet.

BUG FIXES:

o BUG FIX: getAverageFile() of AffymetrixCelSet would average the wrong set of cells if argument 'indices' was different from NULL.

o BUG FIX: Argument '...' to plotDensity() of AffymetrixCelFile and AffymetrixCelSet are no longer passed to identifyCells().

o BUG FIX: calculateResiduals() of ProbeLevelModel would give non-zero residuals for cells not fitted by the PLM.

o BUG FIX: plotNuse() and plotRle() did not handle outliers correctly.

o BUG FIX: Changed default filenames for FIRMA scores to "%s,FIRMAscores.CEL" rather than "%s,FIRMAresults.CEL" for consistency with FirmaModel.

o BUG FIX: extractSnpQSet() would give "Error: object "cleancdfname" not found" if the 'affy' package was not loaded.

o BUG FIX: getCellIndices() in CnChipEffectFile would give "Error in fcn(.subset2(unit, "groups"), ...) : object "odds" not found" for units with other than 1, 2, or 4 groups.

DEPRECATED AND DEFUNCT:

o Replaced argument 'moreCells' with 'ram' and removed argument 'cellsPerChunk' in getAverageFile() of AffymetrixCelSet.

Version: 0.4.2 [2007-02-28]

o Now patches in patches/aroma.affymetrix// are sourced when the package is loaded. To download the latest patches, see the package's group page.

o Added argument 'region' to getUnitsOnChromosome() of the GenomeInformation class.

BUG FIXES:

o BUG FIX: setColorMaps() gave "Error in addColorMap.ArrayExplorer( this, colorMap, ...) : object "nbrOfColors" not found".

o BUG FIX: The output data set as returned by getOutputDataSet() or process() of QuantileNormalization lost the any CDF overridden in the input data set. The only time it did pass down the CDF was when process() was called the first time (so that it actually normalized the arrays). The fix was to make getOutputDataSet() in Transform to pass down the CDF too.

o BUG FIX: process() of ChromosomeExplorer would give an error saying 'Error in file(file, ifelse(append, "a", "w")) ... cannot open file /*****************...'.

Version: 0.4.1 [2007-02-22]

o Fixed the warning about "'tzone' attributes are inconsistent". See code of as.character() for explanation.

o Now fromFiles() of AffymetrixCelSet accepts argument 'chipType' to override any chip type specified in the CEL headers. This is useful in case different CEL files refers to different chip types, which can be the case for mixed generations of CEL files. Also added a scan of chip types.

o Added support for using Windows shortcuts for CDF files, that is, you can use a Windows Shortcut annotationData/chipTypes/Foo/Foo.cdf.lnk to link to annotationData/chipTypes/Bar/Bar.cdf, and whenever using AffymetrixCdfFile to locate the CDF for chip type 'Foo' you will get the CDF for chip type 'Bar', e.g. AffymetrixCdfFile$fromChipType('Foo').

o The annotation labels at the right of all graphics in the ChromosomeExplorer are now made slightly larger.

o Now the table of CNRs generated by the GladModel give links to 'hg17' instead of 'hg18' because 'hg17' is the version of the dChip genome information files, which are the only one currently supported.

o Package passes R CMD check on R v2.4.1 (many empty help pages though).

o Lines of code: grep -v ^# *.R | wc -l => 21772

BUG FIXES:

o BUG FIX: calculateWeights() of ExonRmaPlm now makes sure residuals are calculated first.

o BUG FIX: When creating a monocell, the output did not strip of the tags from the chip type, e.g. annotationData/Foo,core/For,core,monocell.cdf instead of annotationData/Foo/For,core,monocell.cdf.

o BUG FIX: An update to the GladModel class added to previous version would not recognize CEL files with same sample name but different tags to belong to the same sample.

o BUG FIX: calculateResiduals() would erase previously calculated residual files and not re-create them correctly.

Version: 0.4.0 [2007-02-16]

o Package passes R CMD check on R v2.4.1 (many empty help pages though).

o Verified that the current version works on total copy number analysis for combined Nsp & Sty chips. See the aroma.affymetrix group page for the example.

o Added trial version of ExonRmaPlm().

o Added trial versions of ResidualSet() and WeightSet().

o Added test for correct directory structure to fromFiles(). This will enforce users to use the correct structure so that for instance the name of the data set is correctly inferred.

o Added calculateResiduals() to ProbeLevelModel and the ResidualSet and ResidualFile classes.

o Now monocell CDF are names ,monocell.cdf. Before a dash was used instead of a comma. This new style is more in line with the , naming convention used elsewhere in the package. Note: Since there are parameter CEL files referring to the old -monocell, AffymetrixCdfFile$findByChipType() will detect this and look for ,monocell instead. Thus, it should be safe to rename the monocell CDF file.

o Now any annotation file for chip type may be located under annotationData/chipTypes//. This directory structure is preferred, because this will allow you to collect all your annotation files specific to one particular chip type in one place. You may even put the in subdirectories, e.g. Affymetrix/, dChip/ etc.

o From now on all reporters and explorer utilizes the root path reports/, and the path to an image file should be reports/////. The latter subdirectory was added to avoid potential naming conflicts for different reporter or explorer classes.

o Remove package dir doc/. Not used.

o Added writeChecksum() and validateChecksum() to AffymetrixFile to write a checksum file, which later can be validated to the content of the file. This is useful to make sure that transferred files have not been corrected (which happend to HB while transferring via external HDD).

Version: 0.3.6 [2007-02-05]

o Added support to import dChip-exported CEL files. See importFromDChip() in AffymetrixCelSet.

o Now QuantileNormalization() takes an AffymetrixCelFile as a target distribution too, cf argument 'targetDistribution'.

o Now the file cache is organized into subdirectories starting with "aroma.affymetrix/". This makes it easier clear the cache.

o Trial: Added SampleAnnotationFile class. File format is not settled yet.

o Trial: Removed the 4% left and right extension of xlim from the plots and enforced 50px margins outside on both sides. This will make it easier to map the horizontal location in pixels to megabases.

Version: 0.3.5 [2007-01-22]

o BUG FIX: Somehow hgChromosomes.txt disappeared from the last versions of the package. Readded.

o Now fromChipType() of DChipGenomeInformation recognized the Mapping10K_Xba142 genotype information files too, meaning getGenotypeInformation() of AffymetrixCdfFile will also recognize it. Same updates were done for dChip SNP information files.

o Now the default sample of the ChromosomeExplorer is the first sample (and not the 8th, which was left in there while I was debugging). The default chromosome is 1 (not 21st).

Version: 0.3.4 [2007-01-20]

o Passes R CMD check on v2.4.1.

BUG FIXES:

o BUG FIX: When trying to load CDFs (and in some other cases too), the GLAD package (and some other packages) wer loaded although they are only "suggested" packages. This was due to how the constructor of some classes were implemented.

Version: 0.3.3 [2007-01-17]

o Passes R CMD check on v2.4.0.

o Added classes QualityAssessmentModel, QualityAssessmentSet, and QualityAssessmentFile.

o Now createMonoCell() create the CDF in chunks, that is, in constant memory.

o Now plot() of GladModel gets the default 'hgChromosomes.txt' of the package if it can't be found in annotations/.

BUG FIXES:

o BUG FIX: For some reason does clearCache() of Object not clear out all cached fields. Until I've figured out what is wrong, I've added explicit clearCache() to classes using cached fields.

o The FragmentLengthNormalization class forgot to clear cache after cloning input data set. This caused the output data set to get the same average file as the input data set.

o BUG FIX: createMonoCell() of AffymetrixCdfFile would give an errounous mono-cell CDF file due to a recent change.

Version: 0.3.2 [2007-01-07]

o Package pass R CMD check v2.4.0.

o Tested the package from scratch analysis 19 Mapping250K_Nsp and 16 Mapping250K_Sty (15 in common) for total copy-number analysis. Steps involved: quantile normalization, RMA probe-level modelling, PCR fragment-length normalization, and combined GLAD modelling. This was done in WinXP Pro on an IBM X61 with 1.5GB RAM. Memory usage peaked at approximately 1GB.

o Some optimization of what is cached in memory and what is cached on file. Only for some data classes for now.

o Replaced old GladModel with new MultiGladModel, which is now named GladModel.

o Added AffineCnPlm for completeness.

o The ChromosomeExplorer class now generates a complete working ChromosomeExplorer web page.

o WORKAROUND: If 'affy' is loaded after aroma.affymetrix, which happens when loading 'affyPLM', affy will overload the generic function plotDensity() with a regular function breaking that method in aroma.affymetrix. The solution is to make sure 'affy' is always loaded before, which was done by adding 'affy' to 'Depends:' in DESCRIPTION. We have the same problem with the 'oligo' package, which is required by the CrlmmModel class. However, for now, we leave that package under 'Suggests:'.

Version: 0.3.2 [2007-01-06]

o Major changes.

o Renamed all Preprocessing classes to Transform classes.

o Introduced trial version of a top-level Model class in order to minimize repeated code.

DEPRECATED AND DEFUNCT:

o Made several methods "private" in order to hide them form the HTML help tables. Developers should rely on source code and Rdoc comments for now.

Version: 0.3.1 [2007-01-05]

o Package pass R CMD check v2.4.0 (with one warning I suspect is a bug in R CMD check).

o Some code was moved to 'affxparser' (v1.7.3) so it is recommended to update to that as soon as it is available on the Bioconductor servers.

o Added initial code for PLASQ, but more is still needed.

o In addition to default "PM only" model, ProbeLevelModel:s now also handles "PM-MM" models. Note that PM-MM might give a non-positive value. The multiplicate MbeiPlm handles this, but also the log-additive RmaPlm where such values become NAs.

Version: 0.3.0 [2006-12-20]

o Made fitGlad() for classes CnChipEffectFile and CnChipEffectSet deprecated. Use the GladModel class instead.

Version: 0.3.0 [2006-12-08]

o Major updates. See below.

o Change in directory structures. Now all probe-level data is outputted to probeData/, and all PLM data to plmData/. Data from the GladModel is stored to gladData/. Data sets with the same name processed in different ways will be distinguishable by their tags.

o Pre-processing methods have now been split up in two major classes, the ProbePreprocessing and ChipEffectPreprocessing (both inheriting from the Preprocessing class) to indicate that they operate on probe-level and chip-effect data, respectively. All ProbePreprocessing classes output data to the probeData/ directory, and the ChipEffectPreprocessing class to the plmData/ directory.

o ProbePreprocessing classes: QuantileNormalization replaces QuantileNormalizer. AlleleCrosstalkCalibration replaces AlleleCrosstalkCalibrator. PcrProbeCalibration corrects for PCR effects due to oligo sequence and SNP fragment lengths, cf. CRLMM. Adapted from oligo.

o ChipEffectPreprocessing classes: FragmentLengthNormalization to normalize for PCR fragment- length effects after PLM, cf. CNAG.

o Added the PlatformDesign class which provides an interface to a platform-design package without loading the package. This is used for instance by the PcrProbeCalibration class.

Version: 0.2.6 [2006-12-07]

o The recently added methods below makes it possible to store FeatureSet data to CEL files, which will further simplify bridging the aroma.affymetrix and the oligo package.

o Added protected importFeatureSet() to import probe signals from a single-sample oligo::FeatureSet object.

o Added static method createBlankSet() to AffymetrixCelSet to create a set of blank CEL files.

o Added trial version of writeWig() to CnChipEffectSet to export log2 copy numbers to the UCSC Genome Browser.

BUG FIXES:

o BUG FIX: The internal cache for readUnits() of ChipEffectFile classes was not sensitive to neither class nor parameters specific to subclasses.

Version: 0.2.5 [2006-11-22]

o Package pass R CMD check.

o Added GladModel. Now it is fairly simple to estimate total copy numbers from Affymetrix 10K, 100K and 500K data sets.

o Added support for tags to most classes.

o Made encode() and decode() of ParameterCelFile approx 2-3 times faster by skipping the encode-/decodeUnit() step and instead call the encode and decode functions directly. This will speed up the updating of chip-effect files about two times.

o Added R.native to the list of suggested packages. The reason for this is that getAverageFile() of AffymetrixCelSet is using rowMedians(x, na.rm) of R.native. The version in Biobase does not handle missing values. In case R.native is not installed, apply() and median() are used.

o Added SE estimates in RmaPlm from new affyPLM.

Version: 0.2.4 [2006-10-28]

o Added more Rdoc comments.

Version: 0.2.3 [2006-10-23]

o Added gcrma background correction. Contributed by Ken Simpson, WEHI, Melbourne.

o Added extractAffyBatch() to AffymetrixCelSet extracting data applicable to methods in the affy package.

o Added extractSnpFeatureSet() to AffymetrixCelSet and extractSnpQSet() to SnpChipEffectSet extracting data applicable to methods in the oligo package.

o Added trial versions of AffymetrixSnpCdfFile, GenotypeCallFile, GenotypeCallSet etc.

Version: 0.2.2 [2006-09-16]

o Added basic support for dChip genome information. It is good enough though to work with the 100K and 500K SNP chips.

o Package now passes R CMD check. Some cheating were done though, because methods with missing Rdoc where put as \alias{}:es in one place.

Version: 0.2.1 [2006-09-07]

o Another big change in how classes are named.

Version: 0.2.0 [2006-08-25]

o Have done a big redesign of the package. There are now also some basic model fitting algorithm available. Probe-affinity estimates are stored in CEL files. Soon chip effects will also be stored in CEL files using customized CDF files that we very can write using the affxparser package.

Version: 0.1.5 [2006-07-2x]

o BUG FIX: The 'outPath' argument of normalizeQuantile() in the AffymetrixDataset class was not recognized.

Version: 0.1.4 [2006-07-24]

o Important breakthrough: We've update affxparser v1.5.3 with a working updateCel() function to update CEL v4 files. This makes it possible to write normalized probe-level data as CEL files, e.g. now you can use normalizeQuantile(..., format="cel") to generate CEL files. Note that this only works with binary CEL files (v4); ASCII CEL files (v3) and Calvin CEL files (upcoming binary format) is not supported.

o Now findCdf() throws an exception if CDF file is not found.

Version: 0.1.3 [2006-07-05]

BUG FIXES:

o BUG FIX/WORKAROUND: Currently the affxparser code crash R if the file is not a valid CEL file. The best we can do now is to test that the filename has suffix *.CEL. Thanks Ken Simpson, WEHI, Melbourne for pointing this out.

Version: 0.1.2 [2006-06-13]

o Made the static fromFile() and fromFiles() methods more generic such that it is easier to subset the different classes, e.g. for SNP chip classes.

Version: 0.1.1 [2006-05-30]

o Cleaned up the API and the Rd help.

o "Finalized" the quantile normalization.

Version: 0.1.0 [2006-01-11]

o Created.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("aroma.affymetrix")

3.1.1 by Henrik Bengtsson, 10 months ago


http://www.aroma-project.org/, https://github.com/HenrikBengtsson/aroma.affymetrix


Report a bug at https://github.com/HenrikBengtsson/aroma.affymetrix/issues


Browse source code at https://github.com/cran/aroma.affymetrix


Authors: Henrik Bengtsson [aut, cre, cph] , James Bullard [ctb] , Kasper Hansen [ctb] , Pierre Neuvial [ctb] , Elizabeth Purdom [ctb] , Mark Robinson [ctb] , Ken Simpson [ctb]


Documentation:   PDF Manual  


LGPL (>= 2.1) license


Imports methods, R.methodsS3, R.oo, R.cache, R.devices, R.filesets, aroma.apd, MASS, splines, matrixStats, listenv, future

Depends on R.utils, aroma.core

Suggests DBI, gsmoothr, RColorBrewer, Biobase, BiocGenerics, affxparser, affy, affyPLM, aroma.light, gcrma, limma, oligo, oligoClasses, pdInfoBuilder, preprocessCore, AffymetrixDataTestFiles, dChipIO


Depended on by ACNE, REIDS.


See at CRAN