We have released aroma.affymetrix v1.4.0. It is well tested and
validated. Please update:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
What to expect from this release? As an ongoing work we keep
robustifying the code, and now the packages try harder than ever
before to detect user mistakes, errors in data (and code) in order to
prevent mistakes from propagating and contaminating your results. As
usual there were also some bug fixes (nothing serious). The details
are below.
The number one thing on the horizon is support for
technology-independent downstream copy-number analysis. We have
generalized the implementation of the segmentation models (and
plotting) so that they apply to any technology, e.g. Affymetrix,
Agilent and Illumina. It is working, but before releasing all this we
wish to do more real-world large-scale validation and also add
documentation online. But if you're in the copy number business, you
now know what to look forward to in the near future.
More exciting news in the next message...
Henrik & co-developers
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Updates to aroma.affymetrix
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Version: 1.4.0 [2010-01-04]
o BUG FIX: After loading aroma.affymetrix, findCdf() would give "Error in
if (regexpr(pattern, chipType) != -1) { : argument is of length zero",
because AffymetrixCdfFile$findByChipType(chipType=NULL) was not valid.
Now the latter returns NULL without complaining.
o Package passes R CMD check on R v2.10.1 and R v2.11.0 devel and
all of its redundancy tests.
Version: 1.3.6 [2010-01-02]
o Adopted to work with aroma.core v1.3.7 and R.filesets 0.7.0.
o ROBUSTNESS: Using new Arguments$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]
o BUG FIX: 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]
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.
o CLEAN UP: Moved most of AromaUflFile to aroma.core (from aroma.affymetrix).
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Updates to aroma.core
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Version: 1.4.0 [2010-01-04]
o Added trial version of segmentByMPCBS() via the 'mpcbs' package.
o BUG FIX: Added getDefaultFullName() for AromaMicroarrayDataSet and
AromaTabularBinarySet in order to override (parent=1) the new default
of GenericDataFileSet in R.filesets v0.7.0, which would return the
chip type (parent=0) as the name.
o Package passes R CMD check on R v2.10.1 and R v2.11.0 devel and
all of its redundancy tests.
Version: 1.3.8 [2010-01-02]
o Added getPairedNames() to CopyNumberChromosomalModel which returns
combined '<test>vs<ref>' names, e.g. 'TumorvsNormal'. The default
behavior is that if <ref> is the average of a pool, then the
paired name is '<test>', e.g. 'Tumor'.
o CLEAN UP: Moved all GenericSummary code to R.utils.
Version: 1.3.7 [2010-01-01]
o Added argument 'pattern' to byName() for AromaUnitTotalCnBinarySet
and AromaUnitFracBCnBinarySet.
o getSets() of AromaMicroarrayDataSetTuple overrides the default method
by adding the chip types as the names of the returns list.
o CLEAN UP: Removed getSetTuple() from ChromosomeExplorer.
o ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.
o ROBUSTNESS: Now CopyNumberChromosomalModel() asserts that none of the
test samples have duplicated names.
o ROBUSTNESS: Now all index arguments are validated correctly
using the new 'max' argument of Arguments$getIndices(). Before
the case where "max == 0" was not handled correctly.
o BUG FIX: translateFullNames() of ChromosomeExplorer would translate the
full names, but return the original ones.
o BUG FIX: getFullNames() of ChromosomeExplorer reported: Error in
UseMethod("translateFullNames") : no applicable method for
'translateFullNames' applied to an object of class "character".
Version: 1.3.6 [2009-12-08]
o BUG FIX: extractMatrix() of AromaUnitCallFile did not recognize NoCalls.
Version: 1.3.5 [2009-12-02]
o BUG FIX: extractRawCopyNumbers() for RawCopyNumbers would give
an error if the internal logBase was NULL.
Version: 1.3.4 [2009-11-24]
o Moved ChromosomeExplorer to aroma.core from aroma.affymetrix.
o Moved several method for 'profileCGH' objects to aroma.core
from aroma.affymetrix.
o Added extractRawCopyNumbers(, ...logBase=2) to RawCopyNumbers,
which can be used to change the logarithmic base of CN ratios,
if any.
o Added getAverageFile() for AromaUnitTotalCnBinarySet.
o Now all chromosome plot functions have xScale=1e-6 by default.
Version: 1.3.3 [2009-11-19]
o ALPHA: First successful run of segmentation with CbsModel
with AromaUnitTotalCnBinarySet data sets.
o Added isAverageFile() for AromaUnitSignalBinaryFile.
o Added class AromaUnitTotalCnBinarySetTuple.
o GENERALIZATION: Moved CbsModel, GladModel and HaarSegModel
(all segmentation models) of aroma.affymetrix to here.
o GENERALIZATION: Moved all (generalized) ChromosomalModel,
CopyNumberChromosomalModel, and CopyNumberSegmentationModel
from aroma.affymetrix to here.
o Added interfaces CopyNumberDataFile, CopyNumberDataSet,
and CopyNumberDataSetTuple (internal for now).
Version: 1.3.2 [2009-11-12]
o Now AromaUflFile$allocateFromUnitNamesFile() works.
o Added getAromaUflFile() to UnitAnnotationDataFile.
o Moved AromaUflFile to aroma.core (from aroma.affymetrix).
o BUG FIX: importFrom(ufl, dat, ...) where 'ufl' was an
AromaUflFile and 'dat' a GenericTabularFile gave an
error reporting that importFromGenericTabularFile()
is abstract/not defined for AromaUflFile:s.
Thanks Paolo Guarnieri for reporting this.
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Updates to R.filesets
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Version: 0.7.0 [2010-01-02]
o Added protected as.data.frame() to GenericDataFileSetList.
o Now GenericDataFile(NA, mustExist=FALSE) is a valid object.
Made all methods aware of such missing files.
o Now extract(ds, c(1,2,NA,4), onMissing="NA") returns a valid
GenericDataFileSet where missing files are returned as missing
GenericDataFile:s.
o Added na.rm=TRUE to all getTags() so that it returns NULL in case
the file is missing.
o copyTo() of GenericDataFileSet quietly ignores missing files.
o Added Rd help for indexOf() of GenericDataFileSet.
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.
o BUG FIX: Changed the default to 'parent=0' for getDefaultFullName()
of GenericDataFileSet to be consistent with the documentation.
o BUG FIX: Now GenericDataFile(pathname) throws an error if 'pathname'
is referring to a directory.
o BUG FIX: getPath() and getDefaultFullName() of GenericDataFileSet
would return a *logical* instead of *character* value.
o BUG FIX: indexOf(ds, names) of GenericDataFileSet would return a
*logical* instead of an *integer* vector of NA:s if none of the
names existed.
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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