[BioC] LIMMA : design (1, 2, 3, 3 ) , I got EXCITING results, what could be the logic, since i have 2 replicates for 3rd group only ?

[Adaikalavan Ramasamy]

PLEASE correct me if I am wrong. 

You have a total of 4 samples that could be classified into one of 3
groups ? How do you plan on distinguishing biological from technical
variation ? Shouldn't limma come with some sort of warning or error if
there are only one sample per group ?

Regards, Adai



On Tue, 2005-04-26 at 10:01 -0700, Saurin Jani wrote:
> Hi BioC,
> 
> I have 3 groups but I have only 2 replicates for last
> group. so, group 1 and 2 has only one Affy CEL file. I
> Did..LIMMA as below and I got some Exciting results:
> 
> #----------------------------------
> design <- model.matrix(~ -1+factor(c(1,2,3,3)));
> colnames(design) <-  c("g1","g2","g3");
> fit <- lmFit(myRMA,design);
> 
> contrast.matrix <-
> makeContrasts(g1-g2,g1-g3,g2-g3,levels = design);
> 
> fit2 <- contrasts.fit(fit,contrast.matrix);
> fit2 <- eBayes(fit2);
> 
> results <-
> decideTests(fit2,adjust="fdr",p.value=0.01);
> 
> myGenes <- geneNames(myRMA);
> i <- apply(results,c(1,2),all);
> 
> a <- i[,1];
> b <- i[,2];
> c <- i[,3];
> tempgenes1 <- myGenes[a];
> tempgenes2 <- myGenes[b];
> tempgenes3 <- myGenes[c];
> 
> tempall <- c(tempgenes1,tempgenes2,tempgenes3);
> myDEGenes <- tempall;
> 
> esetSub2X <- MatrixRMA[myDEGenes,];
> esetSub2 <- new("exprSet",exprs = esetSub2X);
> pData(esetSub2) <- pData(myRMA);
> heatmap(esetSub2X); 
> #----------------------------------
> 
> I got EXCITING results, what could be the logic,since
> i have 2 replicates for 3rd group only ?
> 
> Could anyone point me out ? 
> 
> I highly appreciate your help , Thank you in advance. 
> 
> Thank you,
> Saurin
> 
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