dear ALL: I can plot the MA pic,but donot know how to use the color. there is a parameter in the function maPlot de.tags. do i need assign each gene a -1,0 or 1 to represent sig down-regulated, no change or up such is the related coding: et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise") summary(de <- decideTestsDGE(et, p=0.05, adjust="BH")) result <- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value") write.table(result,file = "t0h_c0h",sep = "\t") maPlot(logAbundance=unlist(result$table["logCPM"]), logFC=unlist(result$table["logFC"])) -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research 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