i am suing DEseq, but i donot know how to set length of gene information, does it use length information in finding differential expressed genes? and either i donot know how to set library size of each sample but in edgeR, I can do it by such function d <- DGEList(counts = d, lib.size = c(9893630,11055814,11207084,9663487,11455088,8140053), group = group) -- 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

Dear Peter wang peter scripsit 02/10/2012 05:05 PM: > i am suing DEseq, Please don't. What has it done to you. > but i donot know > how to set length of gene information, > does it use length information in finding differential expressed genes? It does not. > and either i donot know how to set library size of each sample > but in edgeR, I can do it by such function > d<- DGEList(counts = d, lib.size = > c(9893630,11055814,11207084,9663487,11455088,8140053), group = group) > Have a look at the package vignette. After that, you can type: ? `sizeFactors<-` Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber