Hi,
aroma.affymetrix v2.2.0 et al. have been released. Make sure to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
The main updates are (with full details below):
FEATURES:
o Added extractExpressionSet() for ChipEffectSet.
o Instead of just throwing "Failed to setup a data set for any of 1
data directories located" when failing to setup a CEL data set, the
error message now also reports *why* it failed with each of the
directories tried.
ROBUSTNESS:
o The Aroma Framework packages are being prepared for getting
namespaces. All underlying R.* packages now have namespaces and for
next release we expect to add them to all aroma.* packages as well. We
take it slow to make sure there are no surprises, but when this is
done you should expect less name clashes of function name, if you are
experiencing any of those.
REPRODUCIBLE RESEARCH:
o The scripts used to build online ACS, UGP and UFL annotation files
are now part of the package distribution, cf.
system.file("buildScripts/", package="aroma.affymetrix").
BUGS:
o As usual, a few bugs have been fixed. See below.
All details on what is updated since previous release is bottom.
Thanks all for the feedback and bug reports - keep'em coming!
Cheers,
Henrik & co-developers
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Updates to aroma.affymetrix
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Version: 2.2.0 [2011-09-01]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.1.9 [2011-08-31]
o Added bpmapCluster2Cdf(), which is a pruned and robustified version
of ditto previously provided by Mark Robinson online. This new
version includes more sanity checks and avoids overwriting existing
CDF files.
o ROBUSTNESS: Now env2Cdf() writes the CDF file atomically by first
writing to a temporary file which is then renamed. It now also
returns the pathname to the CDF written.
o BUG FIX/ROBUSTNESS: getTimestamp() for AffymetrixCelFile would throw
"Error in if (hasTimestamp) { : argument is of length zero" if the
CEL file had a DAT header with a non-standard chip type string, e.g.
an early-access label or no label at all. Updated the local/inner
getTimestampFromDatHeader() of getTimestamp() to also handle such
CEL files. Thanks Irina Ostrovnaya at MSKCC for reporting on this.
Version: 2.1.8 [2011-08-16]
o ROBUSTNESS: If static byName() for AffymetrixCelSet fails to setup
a data set, it now reports the error message for each data set
directory it tried.
Version: 2.1.7 [2011-08-08]
o WORKAROUND: Added similar workarounds as in v2.1.6 for more methods
defined in aroma.core, apply(), rowSums() etc.
Version: 2.1.6 [2011-07-27]
o WORKAROUND: In order for the package to work with the most recent
version of R devel, which automatically add namespaces to packages
who do not have one, we explicitly have specify that this package
should get function such as cat() and getOption() from R.utils
(instead of 'base').
Version: 2.1.5 [2011-07-24]
o Bumped up the package dependencies, especially since R will
soon (in practice) require namespaces for all packages.
Version: 2.1.4 [2011-07-14]
o Added extractExpressionSet() for ChipEffectSet.
o ROBUSTNESS: Added redundancy tests for doRMA() and
extractExpressionSet() for the HG-U133_Plus_2 chip type.
Version: 2.1.3 [2011-06-07]
o ROBUSTNESS: Now the search path is adjusted such that 'ggplot2' comes
after 'aroma.affymetrix', because the former overrides the generic
rescale() function of the latter with a non-generic function.
Version: 2.1.2 [2011-05-26]
o Added an archive of scripts used to build ACS, UGP and UFL annotation
files. The archive is located under buildScripts/ of the package
installation directory and sorted by chip types.
Version: 2.1.1 [2011-04-18]
o DOCUMENTATION: Added more help to createUniqueCdf() for AffymetrixCdfFile.
o DEPRECATED: getUnique() and createUnique() are deprecated.
Use getUniqueCdf() and createUniqueCdf() instead.
o More updates to readGeneAssignments() for AffymetrixNetAffxCsvFile.
o CLEANUP: Dropped argument 'sep' of createMonocellCdf() and
createUniqueCdf() for AffymetrixCdfFile.
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Updates to aroma.core
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Version: 2.2.0 [2011-09-01]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.1.5 [2011-08-30]
o BUG FIX: After introducing a sanity check in aroma.core v2.1.2
(2011-05-11), getSnpPositions() of AromaCellSequenceFile would throw
"Error: length(pos) == ncol(cells) is not TRUE". However, it was not
until aroma.core v2.1.3 (2011-08-01) was release that some people got
problem with this. It turns out that the sanity check catches an
error in how getSnpPositions() of AromaCellSequenceFile allocates
the result vector, a bug that has been there for a very long time.
Luckily, this bug has had no effect on the results for anyone.
Thanks to David Goode (Stanford) and Irina Ostrovnaya (MSKCC) for
reporting on this.
Version: 2.1.4 [2011-08-02]
o The aroma.core v2.1.3 tar ball uploaded to CRAN mistakenly
contained a NAMESPACE file, which shouldn't have been there.
Version: 2.1.3 [2011-07-27]
o WORKAROUND: In order for the package to work with the most recent
version of R devel, which automatically add namespaces to packages
who do not have one, we explicitly have specify that this package
should use cat() and getOption() of R.utils (instead of 'base').
Version: 2.1.2 [2011-07-24]
o Bumped up the package dependencies, especially since R will
soon (in practice) require namespaces for all packages.
Version: 2.1.1 [2011-05-10]
o ROBUSTNESS: Added more sanity checks and more verbose output
to getSnpNucleotides() for AromaCellSequenceFile.
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Updates to R.filesets
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Version: 1.1.0 [2011-07-24]
o Added a namespace to the package, which will be more or less
a requirement in the next major release of R.
--
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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