[BioC] Factorial design with LIMMA

[cmprobst]

>> At 02:23 PM 1/04/2004, cmprobst wrote:
> >
> >First, is this model correct?
>
> Assuming that your strains A and B are different cell types, rather than
> biological replicates of the same cell line, then this looks a correct model.
>

Yes, Strain A and B are different cell types. There are two hybs for each 2x2x2 combination, in a total of 16 hybs (We are going to add another replicate).

These two hybs are biological replicates, that could be included in the model, although I am not interested in them. I have not included them because I was afraid of doing a mistake.

Perhaps, I could model like this, including the covariate "Batch":

design<-model.matrix(~ Batch + Strain*Infected*Time, data=pData(resRMA)

Anyway, thanks for your prompt answer, Gordon.
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