Hi all,
aroma.affymetrix and friends have been updated and is now being rolled
out to the CRAN servers. It is highly recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This update follows the April releases of R v2.11.0 and Bioconductor
v2.6, which we also recommended to use with the aroma framework. In
this release we have added further protection against ending up with
partially written data files due to an abruptly terminated R session.
There were also some bug fixes, which mainly were due to changes in
the new release of Bioconductor that broke some existing methods, e.g.
SNPRMA and CRLMM. Thanks to all users for reporting bugs and other
potential issues. In addition, we have better (although not perfect)
support for gcRMA on more chip types. Affymetrix's recent SNP & CN
chip type Cytogenetics_Array is also better supported. For other
updates and more details, see the end of this message.
Documentation keeps getting added to the http://www.aroma-project.org/
website. As before, any kind of contribution to it is greatly
appreciated.
Cheers,
Henrik & co-developers
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Updates to aroma.affymetrix
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Version: 1.6.0 [2010-05-14]
o Package submitted to CRAN.
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: Added a redundancy test of CRMA "v1.5" for the
Cytogenetics_Array chip type.
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.
o CLEAN UP/DEPRECATED: AffymetrixCelSet$createBlankSet() was removed,
because it has not been used anywhere since 2007.
o BUG FIX: convertToUnique() for AffymetrixCelSet would not recognize
Windows Shortcut links.
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.
o BUG FIX: fit() of CrlmmModel would not work with oligo v1.12.0
and newer.
o BUG FIX: 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.
o ROBUSTNESS: Added redundancy tests for doCRMAv2() and
writeDataFrame().
o BUG FIX: doCRMAv1() for AffymetrixCelSet used undefined 'csN'
internally instead of 'csC'.
Version: 1.5.6 [2010-04-15]
o BUG FIX: 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]
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]
o BUG FIX: allocateFromCdf() of AromaCellCpgFile, AromaCellPositionFile,
and AromaCellMatchScoreFile would drop all but the first tag.
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Updates to aroma.core
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Version: 1.6.0 [2010-05-14]
o Package submitted to CRAN.
o Package pass R CMD check on R v2.11.0 and v2.12.0 devel.
Version: 1.5.8 [2010-05-13]
o Now argument 'path' of all writeDataFrame() methods defaults
to <rootPath>,txt/<dataSet>/<chipType>/.
Version: 1.5.7 [2010-04-27]
o Added writeDataFrame() for AromaUnitTabularBinaryFile.
o Added argument 'columnNamesPrefix' to all writeDataFrame().
o AD HOC: Now getUnitAnnotationDataFile() of AromaPlatformInterface
load aroma.affymetrix if needed and if installed.
Version: 1.5.6 [2010-04-22]
o Added writeDataFrame() for AromaUnitSignalBinary{File|Set}.
Version: 1.5.5 [2010-04-12]
o BUG FIX: getFitFunction() of CbsModel would return a function that
would give "Error in segmentByCBS.RawGenomicSignals(..., seed = seed):
formal argument "seed" matched by multiple actual arguments".
Version: 1.5.4 [2010-04-06]
o Added equals() for CopyNumberRegions.
o Added argument 'seed' to CbsModel, which will, if specified, set
the random seed (temporarily) each time (per sample and chromosome)
before calling the segmentation method.
Version: 1.5.3 [2010-04-05]
o Added argument 'seed' to segmentByCBS() for RawGenomicSignals.
Version: 1.5.2 [2010-03-29]
o ROBUSTNESS: Increased the requirements of support packages.
Version: 1.5.1 [2010-03-02]
o Now segmentByMPCBS() can be used to segment data from a single source.
o CHANGE: Argument 'arrays' of doCBS() for CopyNumberDataSet no longer
subset the input data set, but instead is passed to the fit() function
of the segmentation model. This way all arrays in the input data set
are still used for calculating the pooled reference.
o ROBUSTNESS: Added more sanity checks to segmentByMPCBS() for
RawGenomicSignals.
o BUG FIX: Forgot argument 'verbose' of getOutputSet() of ChromosomalModel.
--
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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