[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.
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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").
JZ
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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