Here is my clean data , I could not post the dput here
Here I try to find up and down regulated genes based on LFQ intensities using limma
design <- model.matrix(~c(rep(1,2),rep(0,2))) fit <- lmFit(data, design) fit2 <- eBayes(fit) myt <- topTable(fit2, coef=2, n=Inf)
which are empty , it is because I don't have any adj.P.Val smaller than 0.05 but I don't know what criteria to select
where do I make mistake ??