[BioC] SAM analysis question

[J. Mcelwee]

  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

**********************************

Joshua McElwee

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