[BioC] Recent changes to Bioconductor packages

[madman at jimmy.harvard.edu]

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.
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04 March 2004: PROcess: Added new package.  JG

04 March 2004: Ruuid - Modified the .Call() calls to meet current standards. JG

04 March 2004: limma 1.5.3.
  - new function smoothVar()
  - source="agilent" added to read.maimages
  - bug fixed in heatdiagram() and heatDiagram() which caused over-printing when using par(mfrow)
  - vennCounts() now uses table() for major computation and is therefore much faster
  - new function FStat()
  - S3 class "classification" replaced by S4 class "TestResults", including 'show' and 'summary'
    methods
  - classifyTests(), classifyTestsT() and classifyTestsP() now produce "TestResults" objects

02 March 2004: annotae - getDOdesc modified in response to changes in the GO 
    data pacakge. The argument "which" can be MF, CC, BP, or ANY. JZ 

02 March 2004: graph - Added a set of coersion functions & methods to convert
    various forms of matrices into graphs.  An adjacency matrix can be 
    directly converted to a garph using 'as', and the functions 'aM2bpG'
    and 'ftM2adjM' have been added as well.  JG

02 March 2004: EBarrays - Added a new contributed package, EBarrays, which
    provides tools for the analysis of replicated microarray data across
    multiple conditions.  JG