[BioC] Limma, model with several factors

[Ingrid Dahlman [guest]]

I have carefully read the Limma users guide but still have not sorted out how I design the contrasts for the following Project.

In want to compare the effect (After vs before) of two different treatments, F and P. The study was carried our in two different centers. This can be illustrated as follows:
 Subject center treatment timepoint
 1            1         F          B
 1            1         F          A
 2            1         P          B
 2            1         P          A
 3            2         F          B
 3            2         F          A
 4            2         P          B
 4            2         P          A
 I want to compare (F.A-F.B)-(P.A-P.B), blocking for subject. However, in addition, I would like to block for center. I.e. the center is like a batch effect.
Is it possible to block for two factors, suject and center, in the same test in Limma?
 /Ingrid

 -- output of sessionInfo(): 

See section 8.7 in the user guide.

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