[BioC] Recent changes to Bioconductor packages

madman at jimmy.harvard.edu madman at jimmy.harvard.edu
Sat Sep 20 06:00:02 MEST 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.
20 Sep 2003: limma 1.2.4
   - ensure that limma passes rcmd check for R 1.8.0
   - fix bug in toptable which affected the displayed A-values
   - new option 'none' for method argument of backgroundCorrect()
   - new argument 'mar' for imageplot().  GKS
18 Sep 2003: factDesign - A new package providing tools for analyzing data
   from factorial designed microarray experiments by Denise Scholtens was
   added.  JG

18 Sep 2003: graph - now uses the install.R mechanism JG

17 Sep 2003: gpls - A new package for multi-group classification using 
   generalized partial least squares by Beiying Ding was included in 
   developmental packages. JZ

17 Sep 2003: MeasurementError.cor - A new package for correlation 
   estimation based on two-stage measurement error model by Beiying Ding 
   was included in developmental packages. JZ 

16 Sep 2003: reposTools - genRepos() will now handle tarballs with 
   a .tgz extension (as opposed to just '.tar.gz'). JG

16 Sep 2003: vsn -    
   1. provides two new methods 'sagmbSimulateData' and 'sagmbAssess' 
   that allow to verify and assess how well vsn estimates the 
   calibration and variance stabilization transformations for data 
   that is in fact distributed according to the two-component model with
   affine array effects (see the SAGMB paper and the vignette.)
   2. better control over the least trimmed sum of squares iterative 
   algorithm in the function vsn through the parameter 'cvg.check' (thanks
   to a suggestion by David Kreil). WH

15 Sep 2003 - added package MAGEML JG

15 Sep 2003 - limma 1.2.0 - fix bug in quantarray read; classifyTests
    now returns F-statistic.  GKS

13 Sep 2003 - SNPtools -- now at version 0.5, stripped down, focusing on bindings
	to XML-RPC facilities of SNPper (snpper.chip.org) -- this
	will go to 1.0 before the next release.  VJC

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