[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Nov 8 11:00:02 MET 2003

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.
Nov 07, 2003: Multiple Packages:  Instances of 'apply(x,1,mean)',
   'apply(x,2,mean') as well as the same for 'sum' were replaced
   with the faster 'rowMean', 'colMean' (and xxxSum).  Packages
   affected:  affycomp, affypdnn, affy, arrayMagic, daMA, gcrma,
   globaltest, gpls, marrayNorm, multtest, pamr, siggenes, 
   and splicegear.  JG

Nov. 06, 2003: annotate: Function lookUp added. lookUp should be used to 
   replace any get and multiget calls to get annotation data from data 
   packages. For example, lookUp("9473672", "hgu95av2", "PMID") or 
   lookUp(c("11706946", "10922468", "10634581"), "hgu95av2", "PMID") 
   should be used istead of get("9473672", env = "hgu95av2PMID") or 
   multiget(c("11706946", "10922468", "10634581"), env = "hgu95av2PMID").

Nov 05 2003: AnnBuilder: Bug fixes for making annotation using LL id as 
   the base map type. JZ

Nov 05 2003: tkWidgets: eExplorer and pExplorer added to allow users to 
   interactively explore R example code or contents of a given data 
   package. JZ

Nov 05 2003: limma 1.3.1.  Bug fix for as.MAList.  Slightly changed comments
   in install.R and aaa.R.  GKS

Nov 04 2003: reposTools - Fixed a bug where packages with a '.' in their
   name were not being registered as part of a repository. JG

Nov 03 2003: CDF Packages - A package for the barley1 chip was contributed
   by Jim MacDonald.  JG

Nov 03 2003: DynDoc - removed the vignette() command as there is now a similar
   function in base that does basically the same thing.  Also the function
   getVignetteKeyword has been added - this can be used to retrieve a
   metadata field from a vignette file (VignetteIndexEntry, VignetteDepends,
   etc).  JG

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