In the output of the heatmap, there are some repeated genes for several times, and I can't figure out why. Obvious, something is wrong.
I try to compare a control group (which is in triplicate: C1, C2, C3) with a treated group which is also a triplicate A (A1, A2, A3), and individually, with another treatment group B (B1, B2, B3). For the sake of example, I had simplified the group's names to letters.
The code that I use for contrast is:
"comparisonmodel <- model.matrix(~0+design)
> colnames (comparisonmodel) <- levels(design)
fit <- lmFit(NmData, comparisonmodel)
#Applying the empirical Bayes method
project.fit.eBayes <- eBayes(fit)
#Make individual contrasts and fit the new model
CaseControl <- makeContrasts(A-C, B-C, levels=comparisonmodel)
CaseControl.fitmodel <- contrasts.fit(fit, CaseControl)
CaseControl.fitmodel.eBayes <- eBayes(CaseControl.fitmodel)
> #Filtering Results
> nrow(topTable(CaseControl.fitmodel.eBayes, coef=1:2, number=1000, lfc=2))
> probeset.list <- topTable(CaseControl.fitmodel.eBayes, coef=1:2, number=100, adjust.method="BH", sort.by="F", lfc=2)"
Is it possible that the repetition of gens in the heatmap to be because of the contrasts?
Here is a link where you can observe the heatmap.