[BioC] SAM for R

[Stephen Eglen]

 > I have been using the affy package to summarize and filter .cel files into
 > expression sets, then exporting these sets into SAM (Significance Analysis
 > of Microarrays) to select differentially expressed genes.  
 > This is getting cumbersome; it would be more straightforward to do
 > everything in R.
 > Does anyone have functions for SAM in R, or can I use any of the existing
 > bioconductor packages to select differentially expressed genes in a way
 > similar to SAM?


hi Thomas, and others,
See the announcement below by Holger Schwender -- the R code works
fine.

Stephen
----------------------------------------------------------------------
 because of the large number of requests I uploaded my functions
 that can perform the SAM analysis and the Empirical Bayes Analysis
 described in the JASA-Paper of Efron to the internet. You can
 download the S-Plus functions from
  
 http://de.geocities.com/holgerschw/GENE-SIG.ZIP
  
 A short description you will find under
  
 http://de.geocities.com/holgerschw/gene-sig.pdf
  
 An older version of the R functions is available at
  
 http://de.geocities.com/holgerschw/r.zip
  
 These R functions cannot handle a very large number of permutations
 (let's say B larger than 500 or 1000). There is a newer version of
 these functions that can handle this number of permutations. I will
 post these functions as soon as I am back home (Sunday or Monday).