[BioC] Advice on experimental setup

[Alex Gutteridge]

On 05.09.2012 09:55, David Westergaard 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.

 From your reply to Sean it's not clear what you mean by this last 
sentence. What are the 'differentially expressed genes for each diet'? 
Any differential expression analysis must compare groups of samples by 
definition, no?

You could compare, say Diet A with the average of Diet B and Diet C (or 
even the average of all three). Is that what you mean? Whether that 
makes any sense depends on your experimental design. Most obviously, is 
one of the the three diets a 'control' diet? If not then would it be 
appropriate to consider an average of the three diets a kind of 
meta-control (probably not a word, but hopefully you know what I mean!)?

-- 
Alex Gutteridge