[BioC] Advice on experimental setup

[David Westergaard]

Hi Alex,

There is no control group as such. One of the diets is somewhat of a
control group, but not quite because it is still a diet that has some
'special' properties. I am used to working with experiments which has
atleast one control group, so this setup is a bit out of my domain,
which is the reason I'm asking this list for advice.

I guess what I meant by 'differentially expressed genes for each
diet', was a list of genes that can be attributed to this exact diet.
Now that I think about it, it may be more appropriate to collect mRNA
at the start, mid and end of the experiment, and measure the change in
each group, instead of comparing these. The experiment is set to run
for 4months. I have not before dealt with experiments which have ran
for so long.
Would the data collected be suited for microarray analysis? And if so,
when should the microarray analysis be performed? When each sample is
collected, or all together at the end?

Best,
David


2012/9/5 Alex Gutteridge <alexg at ruggedtextile.com>:
> 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
>
>
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