[BioC] How to get adjusted p values after "global" fdr correction in decideTests (limma)
paolo.innocenti at ebc.uu.se
Wed Jul 23 12:24:43 CEST 2008
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,
Department of Animal Ecology, EBC
75236 Uppsala, Sweden
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