Hi,
aroma.affymetrix v2.6.0 is available. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release consists mostly of internal framework improvements and
only a few minor updates for the end user, e.g. improvement of the
bpmapCluster2Cdf() method. Of course, there were also a few bug fixes
and updates that make the pipelines faster and more robust overall.
All details are below. It is still highly recommended to update.
Enjoy,
Henrik
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Updates to aroma.affymetrix
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Version: 2.6.0 [2012-09-05]
o Submitted to CRAN.
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
analyses 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]
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.
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]
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: Dropped readCdfDataFrame(), which is identical to
the one in affxparser, which has remained the same since
affxparser v1.21.1 (Oct 2010).
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.
Version: 2.5.7 [2012-08-28]
o SPEED UP: Now doCRMAv2() returns even faster if already processed.
o ROBUSTNESS: Added a 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.
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/<chipType>/.
o BUG FIX: 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 BUG FIX: bpmapCluster2Cdf(..., minNbrOfProbes=n) filtered out units
with less than (n+2L) probes, not n probes as documented.
o BUG FIX: 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.
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.
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Updates to aroma.core
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Version: 2.6.0 [2012-09-05]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.5.14 [2012-09-04]
o Added downloadUGC() for AromaRepository.
Version: 2.5.13 [2012-09-02]
o BUG FIX: interleave() for Image and RasterImage could generate
error 'Error in if (abs(vRatio) > abs(hRatio)) { : missing value
where TRUE/FALSE needed' if odd/even cell intensity columns (rows)
contained all NAs.
Version: 2.5.12 [2012-08-31]
o GENERALIZATION: Now downloadCDF() for AromaRepository downloads
CDFs regardless of *.cdf and *.CDF.
Version: 2.5.11 [2012-08-29]
o ROBUSTNESS: Added argument 'escape' to findAnnotationData(), which
causes such symbols that exist in argument 'pattern' to be
automatically be escaped.
Version: 2.5.10 [2012-08-26]
o DOCUMENTATION: Clarified that when colBinnedSmoothing() is done
over zero-length bins, the output for those bins will be NA.
o BUG FIX: colBinnedSmoothing(..., xOut=xOut) would return binned
values in the incorrect order, iff 'xOut' was not ordered.
Added a systems test for this case.
o BUG FIX: colBinnedSmoothing(..., xOut=xOut) could generate bins
at the ends that did not contain the outer most 'xOut' values.
Version: 2.5.9 [2012-08-22]
o Improved the AromaRepository class.
Version: 2.5.8 [2012-08-21]
o ROBUSTNESS: Now the package startup message is outputted at the
very end. Previously it was done before some additional setup,
which could potentially fail.
o ROBUSTNESS: fitWRMA() and fitWHRCModel() now call rcModelWPLM()
of preprocessCore instead of .Call(..., PACKAGE="preprocessCore").
Doing so will somewhat slow down the speed, because rcModelWPLM()
introduces some non-needed validation of the arguments.
This caused their arguments 'psiCode' and 'psiK' to be dropped.
Version: 2.5.7 [2012-08-08]
o ROBUSTNESS: Added 'preprocessCore' as a suggested package, because
some of the internal functions rely on that package. This was never
an issue, because those functions were called by wrapper functions
in aroma.affymetrix that assert that the package is indeed loaded.
Version: 2.5.6 [2012-07-21]
o Added exportAromaUnitPscnBinarySet() for AromaUnitTotalCnBinarySet.
o Added alpha versions of classes AromaUnitPscnBinary(File|Set).
o Added getNumberOfFilesAveraged() to AromaUnitSignalBinaryFile.
Formely only for AromaUnitTotalCnBinaryFile.
Version: 2.5.5 [2012-07-17]
o Updated package dependencies.
Version: 2.5.4 [2012-07-10]
o Now package imports R.devices, because it uses some of its
device drivers that previously were in R.utils.
Version: 2.5.3 [2012-06-18]
o FIX: Fixed a typo in an error message generated by byChipType()
for several annotation data file classes.
Version: 2.5.2 [2012-05-30]
o Updated package dependencies.
o Added argument 'calculateRatios' to CopyNumberChromosomalModel().
Version: 2.5.1 [2012-04-16]
o CLEANUP: Package now only depends/imports on CRAN package, which
simplifies the installation of aroma.core, and indirectly any
packages that depends on it. Note, there are still "suggested"
non-CRAN packages, which are required by some/optional methods.
o CLEANUP: Package no longer depends on aroma.light, but instead it
"suggests" it. This is possible, because now weightedMad() of
aroma.light has been added to matrixStats v0.5.0.
o CLEANUP: Package no longer "Suggests" affxparser. It was needed because
of the findFiles() function, which has been added to R.utils v1.13.1.
--
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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