I am using edgeR to analyze my RNA-seq data the data is paired-end and strand specific i have 6 sample 1-3 are biological replicate of one tissue 4-6 are biological replicate of the other tissue the problem is for one sample, there are two values, forward expression value and reverse expression value, although most of reverse expression value are zero, due to strand specific experiments but i cannot use only forward expression value for one sample. if i want to keep both forward expression value and reverse expression value, how can i design the model.matrix, thx -- 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