i try to find DE on each time point by comparing treated vs control, such is coding please help me to check if it is right? thank you very much group =factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0 h','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h',' t18h','t18h', 't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48h',' t48h','c6h','c12h','c18h','c36h','c48h')) d <- DGEList(counts = d, lib.size = lib_size, group = group) d <- calcNormFactors(d) #To estimate common dispersion: d <- estimateCommonDisp(d) #To estimate tagwise dispersions: d <- estimateTagwiseDisp(d) #c0h vs t0h et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise") result <- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value") write.table(result,file = "t0h_c0h",sep = "\t") -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253