[BioC] Can subject be treated as fixed effect in linear model with microarray data

[shirley zhang]

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,