[BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)

[Paolo Innocenti]

Hi all,

I used the option "global" in decideTests(), in order to correct for FDR 
  taking into account my 3 contrasts simultaneously.

The list of DE genes I got is longer than the one I get using "separate" 
option (and this should be ok, see here):
http://thread.gmane.org/gmane.science.biology.informatics.conductor/17847

Now, topTable and write.fit implement FDR adjustment with method 
"separate", so if I extract the p.values from these objects, some of 
them, in my situation, will be inevitably higher than 0.05.

How can I get the correct p.values?
Am I missing something obvious?

Thanks in advance for any hints,
paolo



-- 
Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden