[BioC] Limma Contrast Statistics for Affy CEL files,

[Saurin Jani]

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