Happy New Year everyone! I used decideTests in limma to correct for multiple testing across probes and contrasts. I was wondering if there is a way to obtain adjusted p values rather than 1,0,-1 scores. Greetings, Laurens -- ================================================================== Laurens Pauwels DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 GHENT UNIVERSITY/VIB, Technology Park 927, B-9000 Gent, Belgium Vlaams Interuniversitair Instituut voor Biotechnologie VIB mailto:lapau at psb.ugent.be http://www.psb.ugent.be

Hi Laurens, See ?topTable - this may give you what you want, but only for one coefficient/contrast at a time. Also, see ?write.fit - this will give you all the p-values (adjusted if you want) written out to a file that can be opened in Excel; you can also use the results option in write.fit to attach your -1, 0, and 1s from decideTests. Alternatively, if you want an object in R that has both the adjusted p-values and the -1, 0, and 1s, I've been using this code, which I pulled from write.fit: p.value <- as.matrix(fit2$p.value) for (j in 1:ncol(p.value)) p.value[, j] <- p.adjust(p.value[, j], method = "fdr") tab <- list() tab$Genes <- fit2$genes tab$p.value <- p.value tab$Res <- unclass(results) tab <- data.frame(tab, check.names = FALSE) Cheers, Jenny At 09:52 AM 1/3/2006, Laurens Pauwels wrote: >Happy New Year everyone! > >I used decideTests in limma to correct for multiple testing >across probes and contrasts. I was wondering if there is a way >to obtain adjusted p values rather than 1,0,-1 scores. > >Greetings, > >Laurens > >-- >================================================================== >Laurens Pauwels >DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809 >GHENT UNIVERSITY/VIB, Technology Park 927, B-9000 Gent, Belgium >Vlaams Interuniversitair Instituut voor Biotechnologie VIB >mailto:lapau at psb.ugent.be http://www.psb.ugent.be > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu