Hi Naomi,

Thank you very much! Just one more question... what about if I have the two
design 2x2 but in two times (for example at 24h and 48h), I mean, I have two
independent 2x2 designs. Can I analyse together both experiments (using
separate channel) if I want to extract data for the comparison for one
sample at 24h and 48h?.
Thanks!

Luis.

On Mon, Mar 14, 2011 at 10:14 PM, Naomi Altman <naomi@stat.psu.edu> wrote:

> I prefer it.  Theoretically speaking, you should get a bit more power from
> separate channel analysis.
>
> --Naomi
>
>
>
> At 04:53 AM 3/14/2011, Luis A. Alcaraz wrote:
>
>> Hi,
>>
>> I'm trying to analyse data from a microarray experiment which consist in
>> three mutants compared to wild type in a connected design (the
>> experimental
>> design is like in a 2x2 factorial design) with limma.
>> When I do the analysis like in a factorial design (page 45 of the manual)
>> I
>> get a number of differentially expressed genes considerably lower than
>> when
>> I do separate channel analysis (page 50). From a biological point of view,
>> for me it makes sense the new genes that I found with separate channel
>> analysis, but I don't know if this kind of analysis (separate channel
>> analysis with connected design) is right from a statistical point of
>> view. What do you think?
>> Thanks!
>>
>> Luis.
>>
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>>
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>
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