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Sat, 15 Dec 2007
limma
14 December 2007: limma 2.13.2
- update normalizeBetweenArrays(method="vsn") to reflect
changes in the vsn package version 3.4.1.
- additions to the help file for MArrayLM-class objects
plw
Increased z
PGSEA
Fixed a bug in the second vignette...
GeneticsBase
Add as.geneSet.R source file to Collate
Add as.geneSet methods to NAMESPACE
Fix check and warning for alleles argument to makeCCodesAndTTables()
Fix typos
Fix typos
Add as.geneSet() function and documentation
Set pedigree-specific argument founderOnly to be FALSE by default, since it FAILS when pedigree information is not present. TODO: This should be changed to *detech* if pedigree information is present, then act appropriately. Also, correct he default value for confidence interval quantiles to be 2.5% and 97.5% rather than (usually incorrect) 95%.
Minor code reformatting
Fix handling when missing codes are specified by a single 'ALL' entry for all markers
Implement code for remove.spaces=TRUE, convert empty alleles to NA, correct behavior when only one column of genotypes is provided
[/GeneticsBase] permanent link