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Bioconductor Changlog.
Fri, 29 Feb 2008
AnnotationDbi
Cleans up the parameter names and input for SQLForge.
The param "ll" has been changed to "eg" for SQLForge since they are
not called locus link IDs anymore (so why name parameters after a name
people are forgetting in new code?). Also there is an issue that can
crop up with refseq IDs if the user is not paying attention and leaves
on the version numbers to these IDs. For Refseq IDs, only the
accession part of the ID is actually matched to a gene, and some
vendors give IDs that do have the version number attached while others
trim them off. Therefore our DBs always deal with these IDs with the
extraneous stuff removed. However since none of the databases use
these IDs, it also becomes impossible for any database to match on
them if the version numbers have not already been not clipped off by
the user (when the IDs have been provided by a vendor who leaves them
on), so there is now some "auto-cleanup" that SQLForge will do if the
user feeds refseq IDs as a primary ID that are still not trimmed of
their version numbers.
[/AnnotationDbi] permanent link
limma
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
hexbin
Made the following changes:
1) In plotMAhex function require users to specify status explicitly rather than as the component MA$genes$Status to argument MA. (This change allowed hexbin to build again.)
2) Replaced support of soon to be defunct class exprSet with ExpressionSet.
mdqc
Added the new mdqc package to the repository.
gaggle
updated maintainer information
gcrma
Replaced reference to soon to be defunct class exprSet with ExpressionSet.
Ringo
minor changes, mostly naming related
Mfuzz
Replaced reference from soon to be defunct class exprSet with ExpressionSet.
affy
Patch for the bug on se.exprs when subsetting an AffyBatch
(reported by Nicolas Delhomme).
The actual fix differs from Nicolas' patch in the sense that
no new method 'intensity.sd' is added (affy should probably
be on maintenance mode until something unified comes up).
PGSEA
Make two changes:
1) Fixed a typo in PGSEA2.Rnw that was preventing build of package.
2) Replaced support of soon to be defunct class exprSet with ExpressionSet.
marray
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
ppiStats
I have updated sumStatCharts by adding three new functions
made4
Made the following changes:
1) Replaced reference to soon to be defunct class exprSet to ExpressionSet.
2) Used \method tagging in usage section of help files for Sv3 methods.
Biobase
Show correct varMetadata column names when labelDescription is in
a column other than the first
globaltest
Removed support for soon to be defunct class exprSet.