[BioC] design issue arrays

[michela riba [guest]]

Hi, 
I'writing because I have no clear strategy in mind on how to best treat the statistical framework in limma. I have gone through the vignette and user guide and searched the internet, without having a clear answer to my problem.
Practically I have and experiment (triplicate data) with the following:
samples A1, A2, A3 one kind of treatment
samples B1, B2, B3 another kind of treatment
samples C1, C2, C3 the sum of the previous treatments.

The collaboratoras are interested in extracting differences at the level of expression comparing pairwise the sample sets
Besides considering that probably it would have better not doing the C dataset at all
and treat the sum of the A+ B in the contrast matrix in a simple lima, have you a suggestion about this kind of design?
May I consider both the sum in the contrast matrix and the C vs A for example and see if it is more or less the same, should I expect it would be the same?

I thank you very much for your attention and wait for you kind answer,

Michela



 -- output of sessionInfo(): 

> sessionInfo() 

R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.15.2

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