[BioC] extract genes from vennDiagram LIMMA ..How?,

Saurin Jani saurin_jani at yahoo.com
Wed Mar 23 19:48:20 CET 2005

Hi BioC,

For 3 experimental groups in LIMMA, when vennDiagram
is generated based on : 

mask <- c(1,1,1,2,2,3,3,3);
design <- model.matrix(~ -1+factor(mask));
colnames(design) <- c("Group1","Group2","Group3");
fit2 <- contrasts.fit(fit,contrast.matrix);
fit2 <- eBayes(fit2);
ConRow <- nrow(ConX);

#now I am extracting all DE genes from each contrast
and collect it in array, so, later I can draw heatmap
but I have lots of probesets co in that array
for(i in 1:ConRow)
            DEtable <- topTable(fit2,coef = i,number =
numberDE,adjust = "fdr",sort.by = "P");
            DEList[i] <- list(DEtable);
            AllDEGenes <-
            AllDE_FDR <-

For 3 experimental groups, how can someone extract
differentially expressed genes which is common in all
three groups?  

Is it possible to generate vennDiagram() for more than
3 groups..in LIMMA? 

Thank you in advance,

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