Hi,
another year goes by and aroma.affymetrix just turned six years old
and keeps growing. As we speak, a new version of aroma.affymetrix
v2.4.0 and friends is being rolled out on CRAN. As usual, it is
highly recommended to update. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release contains a doFIRMA() wrapper simplifying the alternative
splicing analysis via FIRMA. We have also updated the code such that
it will run faster when processing CytoScanHD_Array data (Affymetrix's
most recent SNP & CN chip). Furthermore, whenever the aroma framework
fails to locate an annotation data file via byChipType(), the error
message thrown is now more informative explaining which file type it
fails to locate. This will help troubleshooting, especially for
beginners. In addition to this, there has been a few bug fixes. All
details are below.
Enjoy,
Henrik
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.4.0 [2012-01-11]
o ROBUSTNESS: Updated package dependencies.
o Adopted a few redundancy tests for the most recent updates.
o BUG FIX: 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.
o CLEANUP: Deprecated doCRMA(). Use doCRMAv1() or doCRMAv2() instead.
o BUG FIX: 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.
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).
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 unnessesary 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.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.4.0 [2012-01-11]
o ROBUSTNESS: Aroma settings are no longer loaded during R CMD check.
o Updated package dependencies.
Version: 2.3.7 [2011-12-22]
o BUG FIX: The overridden library() would always return an invisible()
object, even if base::library() wouldn't. This caused plain library()
to not list installed packaged. Thanks Venkat Seshan at MSKCC for
reporting on this.
Version: 2.3.6 [2011-12-15]
o Now colBinnedSmoothing() handles an unordered 'xOut'.
o Added argument 'units' to writeDateFrame() for AromaUnitSignalBinarySet
to make it possible to write any subset of units and in any order,
e.g. genome order.
Version: 2.3.5 [2011-12-11]
o Now it is possible to fully specify the location and the width
of each bin used by colBinnedSmoothing(), which now also returns
the bin counts as part of the attributes. Moreover, the bins
are now defined to be strictly disjoint using boundaries [x0,x1)
instead of [x0,x1] as before.
o Added plotCoverageMap() for AromaUgpFile.
Version: 2.3.4 [2011-11-19]
o Now byChipType() for UnitAnnotationDataFile and derivatives give an
error message with more information on which file it failed to
locate, e.g. by specifying filename extension it looked for.
o Added default getDefaultExtension() for UnitAnnotationDataFile,
which guesses the filename extension from the class name, unless
overridden by a subclass.
o CLEANUP: Now getFullNames() for AromaMicroarrayDataSetTuple no
longer produces a warning on "is.na() applied to non-(list or
vector) of type 'NULL'".
o BUG FIX: exportTotalCnRatioSet() for AromaUnitTotalCnBinarySet and
exportFracBDiffSet() for AromaUnitTotalCnBinarySet tried to call
cat(verbose, x) with length(x) > 1.
Version: 2.3.3 [2011-11-17]
o Added trial version of AromaUcscGenomeTextFile.
Version: 2.3.2 [2011-11-14]
o BUG FIX: process() of ChromosomeExplorer would throw "Error in
file(file, ifelse(append, "a", "w")) : [...] cannot open file '/
[...] (new Array(': No such file or directory". Importing
the R.rsp namespace in the aroma.core namespace solved this.
Thanks Qian Liu for reporting on this.
Version: 2.3.1 [2011-11-11]
o Added extractPSCNArray() for AromaUnitTotalCnBinary{File|Set}.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to R.filesets
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 1.1.4 [2011-11-19]
o Now more methods for GenericDataFile and GenericDataFileSet handle
so called "empty" files, which are files with NULL pathnames.
--
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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
