Hi BioC, I have basic question regarding How Limma contrast statistics work when I have situation like below:(I am using Affymetrix CEL files, with 4 diff. groups) > design <- model.matrix(~ -1+factor(1,1,1,1,2,2,2,2,3,3,3,4,4,4,4)); > colnames(design) <- c("Group1","Group2","Group3","Group4"); # fitting Linear model to expression set > fit <- lmFit(myRMA_eset,design); > contrast.matrix <- makeContrasts(Group1-Group2,Group1-Group3,Group1-Group4,Group2-Group3, Group2-Group4,Group3-Group4,levels = design); > fit2 <- contrasts.fit(fit,contrast.matrix); > fit2 <- eBayes(fit2); #---get differentially expressed genes(DE Genes) #--I am running for loop to get DE Genes from all possible comparisons for(i in 1:6) { DEtable <- topTable(fit2,coef = i,number = numberDE,adjust = "fdr",sort.by = "P"); DEList[i] <- list(DEtable); AllDEGenes <- c(AllDEGenes,as.character(DEList[[i]][,"ID"])); AllDE_FDR <- c(AllDE_FDR,as.character(DEList[[i]][,"P.Value"])); } Can anyone point to me how contrast statistics work when I compare all possible combinations on design? Thank you so much, Saurin

>Date: Wed, 23 Feb 2005 08:54:41 -0800 (PST) >From: Saurin Jani <saurin_jani@yahoo.com> >Subject: [BioC] Limma Contrast Statistics for Affy CEL files, >To: Bioconductor Bioconductor <bioconductor@stat.math.ethz.ch> > >Hi BioC, > >I have basic question regarding How Limma contrast >statistics work when I have situation like below:(I am >using Affymetrix CEL files, with 4 diff. groups) > > > design <- model.matrix(~ >-1+factor(1,1,1,1,2,2,2,2,3,3,3,4,4,4,4)); > > > colnames(design) <- >c("Group1","Group2","Group3","Group4"); > ># fitting Linear model to expression set > > fit <- lmFit(myRMA_eset,design); > > > contrast.matrix <- >makeContrasts(Group1-Group2,Group1-Group3,Group1-Group4,Group2-Group3 ,Group2-Group4,Group3-Group4,levels >= design); > > > fit2 <- contrasts.fit(fit,contrast.matrix); > > fit2 <- eBayes(fit2); > >#---get differentially expressed genes(DE Genes) >#--I am running for loop to get DE Genes from all >possible comparisons > >for(i in 1:6) > { >DEtable <- topTable(fit2,coef = i,number = >numberDE,adjust = "fdr",sort.by = "P"); > DEList[i] <- list(DEtable); > AllDEGenes <- >c(AllDEGenes,as.character(DEList[[i]][,"ID"])); > AllDE_FDR <- >c(AllDE_FDR,as.character(DEList[[i]][,"P.Value"])); > } > > >Can anyone point to me how contrast statistics work >when I compare all possible combinations on design? Such an open ended question as this is not likely to elicit a useful answer from anyone. The contrast statistics work as claimed in the documentation, and as laid out in the reference Smyth, SAGMB, 2004. What is your question, specifically? Gordon >Thank you so much, >Saurin