I have made a Contrasts matrix as
design <- model.matrix(~0+f) colnames(design) <- levels(f) design fit <- lmFit(eset,design) names(fit) cont.matrix <- makeContrasts(C9T9="Control9-Treated9",C24T24="Control24-Treated24",........................................,levels=design) cont.matrix fit2 <- contrasts.fit(fit, cont.matrix) fit2 <- eBayes(fit2) colnames(fit2) topTable(fit2,coef=1) topTable(fit2,coef="C9T9")
I have total of 8 comparisons and successfully extracted up and down-regulated genes from each comparisons using topTable, beside also identified the total number of up and down-regulated genes from each comparisons using
but I am facing problem to identify/extract common genes that are DE in each of comparisons. Therefore, It is my kind request to all of you, please provides any suggestions for extracting of common genes that are DE in each of the comparisons.