Hi,
aroma.affymetrix v0.9.5 is now available. Please update with:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
The most important update in this release is a major step towards
supporting sequence annotation data and modeling of such. As a
teaser, you will soon be able to do 25-mer nucleotide-position
normalization on any chip type. Otherwise, it contains a few minor
bug fixes, better exception handling and a bit of internal clean up.
The complete update history is below.
Enjoy!
Henrik
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UPDATES to aroma.affymetrix:
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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.
o Renamed getFitFunction() for all PLMs to getFitUnitGroupFunction(),
because the latter is much more explanatory.
Version: 0.9.4.6 [2008-09-19]
o BUG FIX: 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.
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.
o BUG FIX: 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.
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UPDATES to aroma.core:
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Version: 0.9.5 [2008-10-17]
o Package pass R CMD check on R v2.7.2 and R v2.8.0rc.
Version: 0.9.4.5 [2008-10-16]
o BUG FIX: Tried to turn a function passed to as.GrayscaleImage()
in argument 'transforms' to a list using as.list() and not list().
Version: 0.9.4.4 [2008-09-18]
o Added argument 'skip' to writeChecksum() of GenericDataFile.
Version: 0.9.4.3 [2008-09-03]
o Added getSnpPositions(), getSnpShifts(), getSnpNucleotides() and
groupBySnpNucleotides() to AromaCellSequenceFile.
Version: 0.9.4.2 [2008-08-31]
o Update fitGenotypeCone() to support both flavors 'sfit' (old)
and 'expectile' (new).
Version: 0.9.4.1 [2008-08-12]
o Added support for argument 'positions' to countBases() for
AromaCellSequenceFile.
o ALPHA: Added fitMultiDimensionalCone().
o BUG FIX: readSequences() for AromaCellSequenceFile translated
raw values to incorrect nucleotides.
o TESTING: Added redundancy tests to aroma.core.
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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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