[BioC] SAM analysis question

[Sun, Zhifu]

Hi, 

The similar problem has been reported several times at SAM user group email list at Yahoo (
http://groups.yahoo.com/group/sam-software/). Unfortunately I don't know how you can retrieve them from so many emails. The program gives you very different results based on how you order your samples. If you try 1,-1,2,-2,3,-3,4,-4,5,-5 or something like that, you may get different results too. No one at the discussion group has given a good explanation of why the strange behavior happens. I remember one of the creators for the software responded with no explanation but only suggested users to increase their permutations to maximum possible. I ever tried to see if more permutations could get the problem away but never succeed because the program took forever to run if over thousand permutations were used. You may want to try R version of SAM to seen if there is the same problem.


Jeff Sun



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of J. Mcelwee
Sent: Tuesday, March 30, 2004 5:09 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] SAM analysis question


  Hey.  I'm using SAM analysis on paired array data (4 separate pairs, in
two conditions.)  I'm using the SAM excel add-in, and have come across
something a bit disturbing.  Seems that the number of median false
positives changes dramatically depending on how you number the pairs. (for
instance, numbering my 8 arrays: 1,2,3,4 and -1,-2,-3,-4 gives a different
median FDR than numbering them -1,-2,-3,-4 and 1,2,3,4).  i know it's not
strictly a bioconductor question, but i was wondering if anyone else has
run across this and can tell me why this would be the case?  Thanks!
-j

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Joshua McElwee

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