[BioC] Limma Contrast Statistics for Affy CEL files,

[Gordon Smyth]

>Date: Wed, 23 Feb 2005 08:54:41 -0800 (PST)
>From: Saurin Jani <saurin_jani at yahoo.com>
>Subject: [BioC] Limma Contrast Statistics for Affy CEL files,
>To: Bioconductor Bioconductor <bioconductor at 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