HI Daren, Actually, after requests from many of us who do want the all the results from topTable to use in R (and not just written out to a file using write.fit), Gordon kindly made some changes to the newest version of limma out with R 2.8.0 (currently limma_2.16.3). Here's a snippet from the help file: Toptable output for all probes in original (unsorted) order can be obtained by topTable(fit,sort="none",n=Inf). However write.fit or write may be preferable if the intention is to write the results to a file. A related method is as.data.frame(fit) which coerces an MArrayLM object to a data.frame. However, this will only give the adjusted p-values for one contrast at a time, or the over F-stat and adjusted p-values if more than one coefficient is given to topTable. You code below may be better if you want results for all the coefficients together in one object. Cheers, Jenny At 11:10 PM 11/25/2008, Daren Tan wrote: >Hope this helps others > >After I sent out the earlier email, realized that there is >write.fit. My solution is to modify it such that > >fit2tablefunction (fit, results = NULL, file, digits = 3, adjust = >"none", sep = "\t", ...){ if (!is(fit, >"MArrayLM")) stop("fit should be an MArrayLM object") if >(!is.null(results) && !is(results, >"TestResults")) stop("results should be a TestResults >object") if (is.null(fit$t) || is.null(fit$p.value)) fit ><- eBayes(fit) p.value <- as.matrix(fit$p.value) for (j in >1:ncol(p.value)) p.value[, j] <- p.adjust(p.value[, j], >method = adjust) rn <- function(x, digits = digits) if >(is.null(x)) NULL else { if (is.matrix(x) && >ncol(x) == 1) x <- x[, 1] round(x, digits = >digits) } tab <- list() tab$A <- rn(fit$Amean, digits = >digits - 1) tab$Coef <- rn(fit$coef, digits = digits) tab$t <- >rn(fit$t, digits = digits - 1) tab$p.value <- rn(p.value, digits >= digits + 2) tab$F <- rn(fit$F, digits = digits - >1) tab$F.p.value <- rn(fit$F.p.value, digits = digits + >2) tab$Res <- uncla! > ss(results) tab$Genes <- fit$genes return(data.frame(tab, > check.names = FALSE))}> From: daren76@hotmail.com> To: > bioconductor@stat.math.ethz.ch> Date: Wed, 26 Nov 2008 05:00:01 > +0000> Subject: [BioC] Limma: how to get same output as topTable > but for all the genes ?> > > Apology this question is very general, > and no codes to illustrate. How can I emulate topTable to output > all the genes, as topTable is not suitable for outputting all > genes.> > _______________________________________________> > Bioconductor mailing list> Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> Search the > archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >_________________________________________________________________ > > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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@illinois.edu [[alternative HTML version deleted]]