Hello, I am hoping someone will be able to help me with this. I am analyzing the two color common reference design agilent arrays using Limma. I have four replicates and two treatments(control and PCB). I am trying to extract fold change values (PCB/control) for the four replicates separately. lmfit() command after normalizing between arrays is pooling all the samples and I get one fold change value. Is there anyway I can get the values for individual replicates separtely? I want to use the replicate values in Rank Product analysis. Any help will be really helpful. Sorry for bothering everyone with my questions. I have made a lot of progress since I started using this package and it is mainly due to this mailing list. Sincerely, Neel Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607