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Bioconductor Changlog.
Fri, 09 May 2008
AnnotationDbi
More convenient access to author info. via SQLForge wrappers.
This patch makes it easier to add maintainer and author information to
generated packages using the SQLForge wrapper functions.
[/AnnotationDbi] permanent link
biocGraph
updated the dependency on hgu95av2 to hgu95av2.db
limma
8 May 2008: limma 2.15.2
- the following obsolete functions (deprecated Dec 2006 in favour
of read.maimages) are now removed: m.spot, a.spot, read.matrix,
read.series, rg.series.spot, rg.genepix, rg.quantarray, rg.spot
8 May 2008: limma 2.15.1
- bug fix to restore function of plotMA() when object is of
MArrayLM class.
- getEAWP() now gets probe names correctly from the rownames of
exprs when object is of PLMset class.
- edits to read.columns help page to explain that some arguments
cannot be passed to read.table through ... because they are
already used by read.columns.
ShortRead
- likely additional smaller changes looking forward
'pattern' argument of readFastq moved in front of ...
alphabet of alphabetByCycle,BStringSet starts at 1 rather than 0 to
avoid null string warning
logicFS
Removed file/folder
Instead of using the number of correctly classified oob observations, the proportion of correctly classified oob observations can now also be used in the computation of the importances.
Added a file remotely
Removed file/folder
Biostrings
Added the read.liftMask() function for reading a mask of "inter-contig gaps" from an UCSC "lift" file. No version bump.
Fixed the profile calculation method in pairwiseAlignment.
Ringo
some updates, mostly for improved handling ChIP-chip data generated on two-color Agilent arrays
BSgenome
the single sequences stored in a BSgenome object are now masked by the (inactive) built-in masks at load-time (when built-in masks are included in the BSgenome package for this sequence)
Some improvements to forgeMaskFiles(). Version bumped to 1.9.1
annotate
Partial update to the useHomology Vignette.
This partially updates this vignette so that it contains more current
information. This vignette is still not ready for prime time though,
so it is temporarily remaining a .bak file.
affxparser
Add necessary headers to Windows Makefile
lumi
Add smoothScatter option for the pairs and MAplot, and updated related help files and vignette.
Add random seed parameter for the subsetting related functions
graph
fixed a bug