i have two group of samples, each group have 3 biological replicate library(edgeR) library(limma) raw.data <- read.table("111",row.names=1) d <- raw.data[, 1:dim(raw.data)[2]-1 group <- factor(c(rep("sap", 3),rep("vas", 3))) d <- DGEList(counts = d, lib.size = c(9893630,11055814,11207084,9663487,11455088,8140053), group = group) d <- d[rowSums(d$counts) >= length(group)/2,] #normalization d <- calcNormFactors(d) #To estimate common dispersion: d <- estimateCommonDisp(d) #To estimate tagwise dispersions: d <- estimateTagwiseDisp(d) et <- exactTest(d) result <- topTags(et, n=dim(d)[1]+1, adjust.method="BH", sort.by="logFC") write.table(result,file = "DEresult",sep = "\t") Error in data.frame(table = list(logConc = c(-30.7452523676841, -30.9164328563752, : arguments imply differing number of rows: 92305, 1, 2 but write.table(result[1:92304,],file = "DEresult",sep = "\t") can work well and then result[92305,] can also work well: logConc logFC P.Value FDR UN089145 -16.96614 -4.874874e-05 1 1 another problem is the result file "table.logConc" "table.logFC" "table.P.Value" "table.adj.P.Val" "adjust.method" "comparison" "UN038758" -30.7452523676841 -38.5416037522595 1.78446331842105e-37 2.74524811011424e-33 "BH" "sap" "comparison" should include two group name like, "sap" vs "vas" but why only one name? -- 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