Hi all,
new versions of aroma.affymetrix and friends have been released. It
is highly recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
In addition to some added features, there were also a few bugs fixed
in this release. Thanks for the reports! All details on what's new
can be found below.
Cheers,
Henrik & co-developers
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Updates to aroma.affymetrix
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Version: 1.7.0 [2010-07-26]
o Committed to CRAN. No updates.
Version: 1.6.8 [2010-07-21]
o CLEAN UP: Now getAverageFile() for AffymetrixCelSet no longer writes
debug information to ${Rcache}/aroma.affymetrix/idChecks/.
Version: 1.6.7 [2010-07-19]
o Now byPath(..., cdf) for ChipEffectSet will silently try to retrieve
the the monocell CDF if argument 'cdf' is the main CDF. If it fails
an error is thrown. This makes it possible to specify the main/
regular
CDF (or chip type), instead of the monocell CDF, when retrieve a
chip-effect data set.
Version: 1.6.6 [2010-07-02]
o Now AffymetrixCelSet$byName(..., chipType="GenomeWideSNP_6,Full")
will
work (before chiptypes with tags would give an error). This is now
done by first locating the CDF for the chip type (with tags).
o Added doASCRMAv1() and doASCRMAv2() for convenient allele-specific
doCRMAv1() and doCRMAv2() wrappers.
o CLEAN UP: Dropped argument 'transforms' from getImage()
for AffymetrixCdfFile.
Version: 1.6.5 [2010-06-16]
o Added doRMA() for AffymetrixCelSet and data-set names.
doRMA() runs in bounded memory and replicates the results of
fitPLM() in the affyPLM package with great precision.
Version: 1.6.4 [2010-06-07]
o BUG FIX: Added argument shift=+300 to doCRMAv1().
Version: 1.6.3 [2010-05-30]
o Now translateFullName() of AffymetrixProbeTabFile translates
'PROBE_STRAND' to 'targetStrandedness'.
Version: 1.6.2 [2010-05-26]
o Started to add scripts for downloading example data.
Version: 1.6.1 [2010-05-19]
o CORRECTION: doCRMAv1() did not shift +300 the signals before
doing the probe-level summarization.
o BUG FIX: Fixed a bug in PdInfo2Cdf(). Thanks Kasper Daniel Hansen
for reporting this.
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Updates to aroma.core
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Version: 1.7.0 [2010-07-26]
o Committed to CRAN. No updates.
Version: 1.6.8 [2010-07-24]
o Added several methods for CopyNumberRegions, e.g. xRange(),
prune(),
simulateRawCopyNumbers(), "+"(), "-"() and "*"().
Version: 1.6.7 [2010-07-20]
o Added writeDataFrame() for AromaUnitTotalCnBinarySet and
AromaUnitFracBCnBinarySet to get the correct filename extension.
Thanks Nicolas Vergne at the Curie Institute for reporting this.
Version: 1.6.6 [2010-07-19]
o Added subset() for CopyNumberRegions.
o Now extractRegion() for RawGenomicSignals also accepts a
CopyNumberRegions object for argument 'regions'.
o Added extractRegions() for RawGenomicSignals.
Version: 1.6.5 [2010-07-08]
o BUG FIX: writeDateFrame() for AromaUnitSignalBinarySet would
write the same data chunk over and over.
Version: 1.6.4 [2010-07-06]
o BUG FIX: indexOf() for ChromosomalModel would return NA if a search
pattern contained parenthesis '(' and ')'. There was a similar
issue
in indexOf() for GenericDataFileSet/List in R.filesets, which was
solved in R.filesets 0.8.3. Now indexOf() for ChromosomalModel
utilizes ditto for GenericDataFileSet for its solution.
Version: 1.6.3 [2010-06-22]
o BUG FIX: as.GrayscaleImage(..., transforms=NULL) for 'matrix' would
throw "Exception: Argument 'transforms' contains a non-function:
NULL".
Version: 1.6.2 [2010-06-02]
o BUG FIX: updateDataColumn() of AromaTabularBinaryFile would
censor *signed integers* incorrectly; it should censor at/to
[-(n+1),n], but did it at [-n,(n+1)] ("two's complement").
This caused it to write too large values as n+1, which then
would be read as -(n+1), e.g. writing 130 would be censored
to 128 (should be 127), which then would be read as -128.
Added more detailed information on how many values were censored.
Thanks Robert Ivanek for report on this.
Version: 1.6.1 [2010-05-27]
o Added trial version of fullname translator files.
o doCBS() for character:s support data set tuples.
o Added doCBS() for CopyNumberDataSetTuple:s.
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Updates to R.filesets
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Version: 0.8.3 [2010-07-06]
o BUG FIX: indexOf() for GenericDataFileSet/List would return NA if
the search pattern/string contained parentheses. The reason is that
such have a special meaning in regular expression. Now indexOf()
first search by regular expression patterns, then by fixed strings.
Thanks Johan Staaf at Lund University and Larry(?) for reporting
on this issue.
Version: 0.8.2 [2010-05-26]
o Now GenericDataFileSet$findByName(..., mustExist=FALSE) do no longer
throw an exception even if there is no existing root path.
o Added argument 'firstOnly=TRUE' to findByName() for
GenericDataFileSet.
o Added appendFullNameTranslatorBy...() methods to the
FullNameInterface class for data frames, TabularTextFile:s, and
TabularTextFileSet:s.
--
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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