Hi,
today it is five years since the first version of aroma.affymetrix
(v0.1.0) was created. Ever since, the framework has been growing with
new features, support for new chip types and analysis methods
continuously being added. The hope is that the next five years will
add even more to the aroma framework.
Because of the anniversary, we decided to release aroma.affymetrix
v1.9.0 and friends today. It should be on CRAN now (it may take
another day before their OSX binaries show up). Grab the new version
by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
In this release we have added writeCdf() for generating a CDF from
Bioconductor PDInfo package. It replaces the pdInfo2Cdf() function,
with the advantage that an auxiliary CEL file is no longer needed.
Other than that, there are a few bug fixes and some additional
protection preventing mistakes from propagation coming from very
useful feedback from our user and developers forum. For details on
the updates, see below.
Cheers,
Henrik & co-developers
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Updates to aroma.affymetrix
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Version: 1.9.0 [2011-01-10]
o No updates. Submitted to CRAN.
Version: 1.8.3 [2011-01-09]
o Added writeCdf() for AffyGenePDInfo, which replaces pdInfo2Cdf().
An auxillary CEL file is no longer needed to create a CDF from
an PDInfo package. Moreover, contrary pdInfo2Cdf(), the generated
CDF now gets a correct/formal Affymetrix chip type.
o BUG FIX: createMonocellCdf(..., verbose=FALSE) for AffymetrixCdfFile
would still create verbose output.
Version: 1.8.2 [2010-12-04]
o BUG FIX: Local variable 'pdName' of pdInfo2Cdf() was used before it
was defined, which gave an error. Thanks to Guido Hooiveld at
the Wageningen University, Netherlands, for reporting this.
Version: 1.8.1 [2010-11-22]
o ROBUSTNESS: Now extractAffyBatch() for AffymetrixCelSet asserts that
the sample names are unique, which affy::ReadAffy() requires.
Moreover, the sample names are now the fullnames not just the names.
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Updates to aroma.core
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Version: 1.9.0 [2011-01-10]
o No updates. Submitted to CRAN.
Version: 1.8.3 [2010-12-27]
o Added genome annotation file Mouse,chromosomes.txt to
system.file("annotationData/genomes/Mouse", package="aroma.core").
Version: 1.8.2 [2010-12-07]
o ROBUSTNESS: Whenever the GLAD package is tried to be loaded and it
fails due to failure of loading a shared library, then this will be
remembered for 24 hours while it will not be loaded again.
o Added requireWithMemory().
Version: 1.8.1 [2010-12-02]
o BUG FIX: plot() for CopyNumberSegmentationModel would throw exception
"Cannot infer number of bases in chromosome. No such chromosome: 25"
for chromosome 25.
o BUG FIX: drawCytoband2() would throw an error if argument 'cytoband'
was an empty data frame, which could happen if there is no cytoband
annotation data for the requested chromosome. Now it returns quietly.
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Updates to R.filesets
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Version: 0.9.1 [2010-11-19]
o ROBUSTNESS: Now GenericDataFileSet$byName() asserts that arguments
'name' and 'tags' contain only valid characters. This will for
instance prevent passing paths or pathnames by mistake.
o Now appendFullNameTranslator(..., df) for FullNameInterface takes
either 'pattern' or 'fixed' translations in data.frame.
--
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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