Dear All,
I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams.

The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2.

I am certain it is a small glitch somewhere at my end that i get zero counts for my summary(decideTests). Please find below my code and i would really appreciate any help here at all.

Thanks,
Ekta
## R Script ###
> numGenes <- nrow(eset)
> library(limma)
> samples <- c("Un","Un","DMSO10","DMSO10","DMSO5","DMSO5");
> fl <- as.factor(samples)
> design <- model.matrix(~ 0+ fl)
> colnames(design) <- levels(fl)
> fit <- lmFit(eset, design)
> cont.matrix <- makeContrasts(DMSO10-Un, DMSO5-Un, levels=design)
> fit2 <- contrasts.fit(fit, cont.matrix)
> fit2 <- eBayes(fit2)
> tTUni<- topTable(fitUni, adjust="fdr", sort.by="B", number=numGenes)
> results <- decideTests(fit2)
> vennDiagram(results,include=c("up","down"),counts.col=c("red","green"))
## ### I get zero genes for upregulation and downregulation #####


Senior Research Associate
Bioinformatics Department
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