[BioC] Advice on experimental setup

[David Westergaard]

Pardon the spam, I forgot to include the list.

Best,
David

2012/9/5 David Westergaard <david at harsk.dk>:
> Hi Sean,
>
> Groups 1, 2 and 3 are no different except for the diet being fed.
>
> Best,
> David
>
> 2012/9/5 Sean Davis <sdavis2 at mail.nih.gov>:
>>
>>
>> On Wed, Sep 5, 2012 at 4:55 AM, David Westergaard <david at 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