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Bioconductor Changlog.
Fri, 11 Jul 2008
limma
11 July 2008: limma 2.15.10
- Better treatment of array weights in linear model functions.
lm.series() and gls.series() now treat array weights as a
special case, when there are no missing values in the expression
data and now probe-specific weights. This means that the array
weights are now incorporated into fit$cov.coefficients, meaning
that constrasts.fit() will correctly take array weights into
account when computing contrasts standard errors. It also means
that lmFit() is much faster when array weighting is used.
flowCore
fixed inconsitencies in the splitting methods
Biostrings
Add more information to PairwiseAlignmentSummary show output.
Minor change to mismatchSummary function.
Created a PairwiseAlignmentSummary class to make it easier for users to get summaries of fitted pairwise alignments.
Added nmatch and nindel functions.
Added a weight argument to mismatchSummary function.
Minor change to man page.
Minor speedup to mismatchSummary method for PairwiseAlignment objects.
GEOquery
2.5.3
-----
Thanks to Jonathan Dreyfuss for suggesting a change to deal with 'null' in GSEMatrix files
* Added na.strings=c('NA','null','NULL') to the parseGSEMatrix read.delim() call
PGSEA
Fixed aggregateExprs() to work with ".db" annotation packages...
xcms
added -DWIN32_LEAN_AND_MEAN to Makevars.win to fix ramp build on windows