On Wed, Sep 5, 2012 at 4:55 AM, David Westergaard <david@harsk.dk> wrote:

> 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?
>

Hi, David.

Are groups 1, 2, and 3 different, or do they differ only in the diet being
fed?

Sean

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