[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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19 Mar 2004: affy 1.4.21 (this reports changes that happened during the very
  last versions).  LG 
  - the pack needs R-1.9.0-to-be-released (a fairly recent R-devel is enough).
  - the deprecated option 'xy' in indexProbes (and friends) was removed. 
  - the xy coordinates starting at one (but not at zero) complication has
  been sorted out (package-wide option introduced as a global switch)
  - fixed issue with computeExprSet when querying unknown affyids (no
  longer crashes).
  - better handling or errors when running computeExprSet
 
17 Mar 2004: altcdfenvs - A package to help building alternative associations
  between identifiers and probes on microarrays. The code and examples apply 
  directly to Affymetrix data. The vignette provides a step-by-step tutorial
  to go from a given set of reference sequences in a FASTA file to a cdfenv
  to be used with AffyBatch objects.  LG
 
16 Mar 2004: limma 1.5.7.  GKS
- Sweave-style vignette added, as well as User's Guide
- new function array2channel() to convert targets files from by-array to by-channel representation
- removed warning about Cy3, Cy5 columns from readTargets()
- more general use of 'ref' in modelMatrix(), doesn't have to occur on every array
- target names are sorted in modelMatrix()
- designMatrix() renamed to modelMatrix(), designMatrix() deprecated
- new function lmsc.series() for single-channel linear models

15 Mar 2004: Biobase - modified the openVignette code to use the new .rds
   metafiles instead of the 00Index files.  JG