[BioC] SAM for R

[James MacDonald]

You will not be able to download the scripts from that page any longer.
Holger took them down after being counseled that he may be in legal
trouble given that there are patents pending on the SAM algorithms. 

My understanding is that he contacted Rob Tibshirani for permission to
post the scripts but has not received an answer.

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Stephen Eglen <stephen at inf.ed.ac.uk> 06/04/03 05:41AM >>>

 > 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).

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor