That works! Thank you, paolo Gordon K Smyth wrote: > Dear Paolo, > > What you say is correct. The only way to get the adjusted p-values to > go with method="global" is > > adj.p <- p.adjust(fit$p.value, method="BH") > > where 'fit' is the fit object that you gave to decideTests(). > > Best wishes > Gordon > >> Date: Wed, 23 Jul 2008 12:24:43 +0200 >> From: Paolo Innocenti <paolo.innocenti at="" ebc.uu.se=""> >> Subject: [BioC] How to get adjusted p values after "global" fdr >> correction in decideTests (limma) >> To: AAA - Bioconductor <bioconductor at="" stat.math.ethz.ch=""> >> >> 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 >> Norbyv?gen 18D >> 75236 Uppsala, Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden