Hi list; I am sorry if this topic is too old, since I did read lots thread in BioC maillist. But it seems that agreement is not yet reached. My questions are: (1) Do we need to filter genes with low expression before applying any formal analysis. This step is gonna introduce additional error into final result, but will it bring more benefit? (Personally I think we should based on a time-course experiment we have done) (2) If so, which method is the best or better to use? Or is there any general steps we would adopt to find a method to filter genes? Especially in the case with low replication for each condition. ( For the time-course experiment I mentioned above, genes with different profile patterns from different normalization method are ignored) Any comment is welcome! Fangxin -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu