[BioC] DESeq: GLM for multi-factor and mulit-level designs

[Dorota Herman]

Hello everyone,

I am currently working on GLM for RNA-seq data in DESeq for a design 
with two factors and three factor levels, such as:

type experiments
A_1 A exper1
A_2 A exper2
A_3 A exper3
B_1 B exper2
B_2 B exper3
B_3 B exper4
C_1 C exper4
C_2 C exper2
C_3 C exper1

In the recent example of the GLM application there is a fixme note:

“Can we add a paragraph on what to do if we only want to make specific 
comparisons, e.g. let fac be a factor with three levels A, B and C, and 
we want to test pairwise for differences between A and B (without C), 
between A and C (without B) etc.” .... and between B and C (without A)

Is it possible to conduct such a analysis with the current DESeq version?

Thanks a lot
Dorota

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==================================================================
Dorota Herman, PhD 
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927
9052 Gent, Belgium
Tel: +32 (0)9 3313692
Email:dorota.herman at psb.vib-ugent.be
Web: http://www.psb.ugent.be