Hi Bioconductor users; I have a general question about limma model. In limma package, usually one linear model applies to all genes, and error variances from all genes are modified simultaneously. What if some factors, for example, one main effect, is only significant for some genes. Then if we want identify genes based on the significance of another main effect (of interest). What is the best way to do it? Currently I juse leave this factor in the model which is applied to all genes, but this might under-estimate the total number of genes on which the effect of interest is significant. I am sorry if this question has been asked/answered here before, I wouldn't find it through searching the archive. Any comment, suggestion or experience is appreciated. 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