[BioC] fdr adjustment in limma

[Kimpel, Mark W]

How does the method "fdr" in limma work? Strictly speaking, I am not
aware that fdr methods actually adjust p values but rather set p value
cut-offs according the a value q, the user defined acceptable proportion
of false positives. The set of all tests with a p value less than or
equal to the cut-off would be expected to have a false positive rate of
the value q.
 
I have played around with limma's fdr method a bit and I get the feeling
that, after fdr correction using p.adjust, perhaps I should set my own p
value tolerance equal to my FDR tolerance. In other words, if I am
willing to accept an FDR of 10%, after applying p.adjust, I should
accept all tests with p<0.10 as significant.
 
Am I right or wrong on this?
 
Thanks,
 
Mark
Mark W. Kimpel MD
 
Official Business Address:
 
Department of Psychiatry
Indiana University School of Medicine
Biotechnology, Research, & Training Center
1345 W. 16th Street
Indianapolis, IN  46202
 
 

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