Hi all,
aroma.affymetrix v2.9.0 has been released and is available on CRAN
(where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This is mainly a maintenance update to meet some new CRAN
requirements. Interestingly, no bugs where found/reported since
January (not to say there aren't any left). Details on what's updates
can be found below. The only thing I'd like to point out is that the
"everything-in-one-go" pipeline methods doRMA(), doGCRMA(), doFIRMA(),
doCRMAv2() etc now have help pages, e.g. ?doRMA.
...and don't forget to update to R v3.0.0.
Happy spring/fall wherever you are,
Henrik
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Updates to aroma.affymetrix
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Version: 2.9.0 [2013-05-02]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.8.4 [2013-05-02]
o DOCUMENTATION: Now doRMA(), doGCRMA(), doFIRMA(),
doCRMAv1()/doASCRMAv1() and doCRMAv2()/doASCRMAv2() are
fully documented and listed in the help index.
o Added argument 'annotationPkg' to extractExpressionSet() for
ChipEffectSet, which (indirectly) sets the 'annotation' slot
of the returned ExpressionSet.
o Added extractFeatureSet() for AffymetrixCelSet.
o SPEEDUP: Added ^Cyto.*Array$ to list of SNP chips that isSnpChip()
for AffymetrixCdfFile knows of without having to scan the CDF.
o SPEEDUP: Just as doCRMAv2()/doASCRMAv2(), now also doRMA() and
doGCRMA() return much quicker if already processed.
o CLEANUP: Removed argument 'ram' from doNnn() methods in favor
setOption(aromaSettings, 'memory/ram', ram).
o CLEANUP: Made several deprecated methods defunct.
Version: 2.8.3 [2013-04-01]
o Force creation of a generic process(), because depending on the version
of R.rsp at the time of the build, process() may be missing or not.
o Bumped up package dependencies.
Version: 2.8.2 [2013-03-22]
o Obscufated the error message on ASCII CDFs on how to change settings
to allow the processing of such, because it shouldn't be easy to do that.
Version: 2.8.1 [2013-03-05]
o DOCUMENTATION: Updated the help usage section for all static methods.
o Bumped up package dependencies.
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Updates to aroma.core
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Version: 2.9.0 [2013-04-23]
o No updates.
o Bumped version for CRAN submission.
o Package passes all redundancy tests.
Version: 2.8.7 [2013-04-22]
o CLEANUP: Package no longer try to apply package patches, which
was only possible when namespaces where not used.
o CLEANUP: Package no longer depends on R.cache (only imports it).
Version: 2.8.6 [2013-04-21]
o CLEANUP: Made is(Homo|Hetero)zygote() and getPhysicalPositions()
defunct.
Version: 2.8.5 [2013-04-08]
o Updated package dependencies.
Version: 2.8.4 [2013-03-28]
o Added the sqrtsign() transform. This makes it possible to plot
log2 PLM residuals (in aroma.affymetrix) on a blue-to-red scale using
setColorMaps(.., "log2,sqrtsigned,bluewhitered") where
bluewhitered <- colorRampPalette(c("blue", "white", "red")).
o Bumped the package dependencies.
Version: 2.8.3 [2013-03-23]
o Bumped the package dependencies.
o Added an Authors@R field to DESCRIPTION.
Version: 2.8.2 [2013-03-05]
o DOCUMENTATION: Updated the help usage section for all static methods.
o Bumped up package dependencies.
Version: 2.8.1 [2013-01-03]
o CLEANUP: Deprecated nbrOfArrays() for AromaMicroarrayDataSet and
AromaUnitTotalCnBinarySet.
o CLEANUP: Some of the internal aroma.core code still called
deprecated methods resulting in unneccessary warnings.
--
--
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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