[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Apr 10 11:00:02 CEST 2004

This is an automated message sent out weekly to report recent changes
to Bioconductor packages.  Please see the URL 
http://www.bioconductor.org/changelog.html for a complete history of 
changes.  Unless otherwise noted, these changes apply to the developmental
packages only.
7 April 2004: limma 1.6.1.  GKS
- fix to printHead to treat factors as as vectors
- new argument cex for vennDiagram

6 April 2004: limma 1.6.0.  GKS
- additional argument block to duplicateCorrelation, gls.series and lmFit to treat
  technical replicates as randomized blocks
- new methods Rquantile, Gquantile, Tquantile for normalizeBetweenArrays()
- lmFit now extracts probe IDs from exprSet object
- Ecoli-lrp case study added to User's Guide
- backgroundCorrect(,method="edwards") now handles NAs
- bug fixes to backgroundCorrect(,method="edwards")
- classifyTests() renamed to classifyTestsF()
- classifyTestsP() now extracts degrees of freedom from object
- read.maimages no longer disallows source= and columns= together

23 March 2004: reposTools - added support for package bundles.  JG

20 March 2004: limma 1.5.8.  GKS
- internal links added to contents section of User's Guide
- changed calling sequence in duplicateCorrelation() to randomizedBlockFit(),
  limma now depends on package statmod >= 1.0.6
- two changes to plotPrintTipLoess() to avoid warning messages
- bug fix to duplicateCorrelation() to avoid test on rho[i] when NA

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