Dear Bioconductor, In a microarray data, there are 20 subjects grouped by Gender, each subject has 2 tissues (normal vs. cancer). In fact, it is a 2-way anova (factors: Gender and tissue) with tissue nested in subject. I've tried the following: Model 1: lme(response ~ tissue*Gender, random = ~1|subject) Model 2: response ~ tissue*Gender + subject Model 3: response ~ tissue*Gender It seems like Model 1 is the correct one since my experiment design is nested design. However, I got a few significant genes for Gender effect from Model 1 so I want to use Model 2 or Model 3. Can anybody tell me whether Model2 is completely illegal? Thanks,