[BioC] analyze three factors in Limma

[Gordon K Smyth]

Dear Ingrid,

> Date: Thu, 16 May 2013 19:57:37 +0000
> From: Ingrid Dahlman <Ingrid.Dahlman at ki.se>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] analyze three factors in Limma
>
> Hi!

> I would in a microarray experiment analyze three factors simultaneously 
> in Limma, treatment, group (i.e. gender), and study center.  Is it 
> possible to include three factors simultaneously in an interaction 
> model?

It's easy to include three, or indeed any number, of factors in a limma 
model.

> Can I use the "sum to zero" parameterization as described in Section 
> 8.5.4 of the user guide?

You could, but why would you want to?

> Any more specific recommendation on how to proceed?

Hard to give any specific advice on the basis of the information you give. 
However, if you are not familiar with setting up model formula in R for 
factorial experiments, then the limma User's Guide strongly recommends 
that you setup your experiment as a oneway layout as per Section 8.5.2. 
This works for any number of factors.

Best wishes
Gordon

> /Ingrid

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