I had a few quick questions about the limma models. The first is when writing these to a file, the fold changes would be the "Coef" column, not the A column, which is the average across all of the arrays? The second is when I write my bayes model to a file, it only attaches the probe ID, I wanted to see if there was a way to attach the remaining gene annotation but the limma documentation isn't clear on how to accomplish that. Here is how I am currently performing the fitting: contmat <- makeContrasts(d-s, levels = design) fit1 <- lmFit(x[[1]]$avg$E, design) fit2 <- eBayes(contrasts.fit(fit1, contmat)) diff <- topTable(fit2, coef = 1, adjust = "BH", genelist = x[[1]]$avg$genes ) res <- decideTests(fit2) comp <- vennDiagram(res) write.fit(fit1, results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "lmfit.csv"), collapse = "")) write.fit(fit2, results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "be.csv"), collapse = "")) where x[[1]]$avg is the corrected, normalized, replicate averaged array. Here is some example output from write.fit(fit2...): A Coef t p.value F F.p.value d - s 10.99 5.352 6.82 6.00E-04 46.55 6.00E-04 0 12.48 5.347 14.13 1.00E-05 199.78 1.00E-05 1 12.84 4.775 11.99 3.00E-05 143.65 3.00E-05 1 13 4.646 10.98 5.00E-05 120.49 5.00E-05 1 Joseph Cornish Post-Bac IRTA NIAID EVPS [[alternative HTML version deleted]]

Hi Joseph, It's correct that "the fold changes would be the "Coef" column, not the A column, which is the average across all of the arrays". These are in log2 scale. Regarding other annotation of probe IDs, I will firstly check "names(fit)". If there is fit$genes or fit$genes$IDs, and the anno file has the columns of IDs, GeneNames, and ReSeq, code as the following. m<-match(fit$genes$IDs, anno$IDs) fit$genes$symb<- GeneNames[m] fit$genes$refseq<- ReSeq[m] .... data.frame(fit) [1:2,] # this dataFrame has all anno information you have added to fit$genes. Hope this help. Cheers, Di ---- Di Wu Postdoctoral fellow Harvard University, Statistics Department Harvard Medical School Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA ________________________________________ From: bioconductor-bounces@r-project.org [bioconductor- bounces@r-project.org] on behalf of Cornish, Joseph (NIH/NIAID) [F] [joseph.cornish@nih.gov] Sent: Wednesday, April 03, 2013 1:35 PM To: bioconductor at r-project.org Subject: [BioC] Limma linear models I had a few quick questions about the limma models. The first is when writing these to a file, the fold changes would be the "Coef" column, not the A column, which is the average across all of the arrays? The second is when I write my bayes model to a file, it only attaches the probe ID, I wanted to see if there was a way to attach the remaining gene annotation but the limma documentation isn't clear on how to accomplish that. Here is how I am currently performing the fitting: contmat <- makeContrasts(d-s, levels = design) fit1 <- lmFit(x[[1]]$avg$E, design) fit2 <- eBayes(contrasts.fit(fit1, contmat)) diff <- topTable(fit2, coef = 1, adjust = "BH", genelist = x[[1]]$avg$genes ) res <- decideTests(fit2) comp <- vennDiagram(res) write.fit(fit1, results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "lmfit.csv"), collapse = "")) write.fit(fit2, results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "be.csv"), collapse = "")) where x[[1]]$avg is the corrected, normalized, replicate averaged array. Here is some example output from write.fit(fit2...): A Coef t p.value F F.p.value d - s 10.99 5.352 6.82 6.00E-04 46.55 6.00E-04 0 12.48 5.347 14.13 1.00E-05 199.78 1.00E-05 1 12.84 4.775 11.99 3.00E-05 143.65 3.00E-05 1 13 4.646 10.98 5.00E-05 120.49 5.00E-05 1 Joseph Cornish Post-Bac IRTA NIAID EVPS [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor