Hi, One quick question. I have an expression data set mydata.eset. I build up the design and contrast matrix as follows. contrast.matrix <- design.pairs(c(group)) # design pairs is a quick function to do it automatically fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) results <- decideTests(fit2) Ok so far so good, it works Now i want to compute a tukyHSD test between the same groups. It is not possible to use the fit object directly , how would you do that from your eset object and design matrix ?? thanks, david