[BioC] Advice on experimental setup

[David Westergaard]

Hello,

I am assisting in the setup of an experiment, in which 3 groups, each
consisting of 8 subjects, will be fed 3 diets:
Group 1 - Diet A
Group 2 - Diet B
Group 3 - Diet C

We plan on using limma to identify the differentially expressed genes.
Reading the limma users guide, a factorial design matrix seems to be
appropriate. I am, however, wondering if we, by using this setup, can
elucidate the differentially expressed genes for each diet, and not
just the ones between groups, e.g. when comparing Group 1 - Group 2.

What is your advice on this?

Thanks in advance!

Best regards,
David Westergaard