that is what i understand about model matrix please tell me if it is right? thank you very much > Treatment <- factor(targets$ Treatment, levels=c("Control","Treatet")) > Time <- factor(targets$Time, levels=c("0","6")) > design <- model.matrix(~Treatment* Time) Coefficient Comparison Intercept Control.0 TreatmentTreatet Treatet.0- Control.0 Time6 Control.6- Control.0 TreatmentTreatet: Time6 (Treatet.6-Treatet.0)-( Control.6- Control.0) > design <- model.matrix(~Time *Treatment) Coefficient Comparison Intercept 0.Control Time6 6.Control -0.Control TreatmentTreatet 0.Treatet -0.Control Time6: TreatmentTreatet (6.Treatet -6.Control)-(0.Treatet -0.Control) -- 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