[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 ?

[Saurin Jani]

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