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Bioconductor Changlog.
Tue, 26 Feb 2008
AnnotationDbi
Updates to SQLForge and a better error msg for mget.
Part of this update just changes the AnnotationDbi mget message to
look more like what is expected based on what its parents msg looked
like. The other part overhauls the part of the code that does the
initial mapping for SQLForge so that it will not write out
indermediate files. This step was uneccessary and generally just a bad
idea that was causing bugs on the windows platform. The new code
should be more robust to cross platform issues.
[/AnnotationDbi] permanent link
oligoClasses
added method to coerce SnpCallSetPlus to oligoSnpSet. Added functions calculateCopyNumber and affyPlatforms
[/oligoClasses] permanent link
genefilter
Removed methods for soon to be defunct exprSet class.
Biostrings
Added the 'collpase' arg to alphabetFrequency() and family. Version bump.
GeneMeta
Remove methods for soon to be defunct class exprSet.
ArrayExpress
?\195?\130?\194?\163Change default tempoutdir
[/ArrayExpress] permanent link
gpls
Two changes:
1) Removed methods for soon to be defunct class exprSet.
2) Cleaned up WARNINGS related to predict.gpls method definition.
PGSEA
Fixed a bug in enforcing the size of the concepts to be tested in PGSEA()
Added "enforceRange" argument to PGSEA()
Added "grid line type" argument to smcPlot()
geneplotter
Removed methods for soon to be defunct class exprSet.
buildBioC
small fix
xcms
Adapted path in vignette to new directory structure in msdata
exonmap
Added explicit error message to gene.strip when no exon probesets remain after filtering for multi- and exon-targeting
Added explicit error message to gene.strip when no exon probesets remain after filtering for multi- and exon-targeting
BiocCaseStudies
a couple of glitches, hopefully repaired
[/BiocCaseStudies] permanent link