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

Paolo Innocenti paolo.innocenti at ebc.uu.se
Wed Jul 23 12:24:43 CEST 2008

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):

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

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