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Bioconductor Changlog.
Wed, 30 Apr 2008
Category
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Category
added doc pages to pass check
Category
bugfix to handle NA p-values
Category
bugfix, and bumped version
update to include effect sizes in linear model test output
Category
updated version
Category
added a t() that was missing
Category
fixed up the KEGG part so it now works with the org.XX.eg.db packages
Category
fixed a bug reported by Paul Evans, where a zero-length list of categories
induced a whole bunch more zero length vectors and caused no end of problems
with computation of the odds ratio etc
Category
Replace the usage of now defunct phenoData class with AnnotatedDataFrame.
Category
trying to move to the new DB packages, and added a NEWS file
Category
used makeChrBandInciMat directly instead of MAPAmat since we already have the chr band graph
Category
a first stab at documentation
checked in code for 'linear model' enrichemnt test, currently for chr bands only
Category
minor change to get this pushed
minor change to the vignette
Category
Updating the license reference to reflect R standards.
Category
Fixed breakage introduced by DB schema changes in AnnotationDbi (we recently moved from using old 0.9 schemas to new 1.0 schemas). The package still doesn't pass R CMD check for me but at least GOstats does now (not sure the remaining problems are related to the DB schema changes). Version bump anyway.
Category
I fixed and documented the behaviour of cateGOryMatrix in cases where 'categ' contains GO categories unknown to the GO package.
The error in R CMD check:
Error in v1[sapply(v1, function(z) !any(is.na(z)))] :
invalid subscript type 'list'
Calls: MAPAmat -> makeChrBandInciMat
was already there and it would be nice if its author could fix it.