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Old 04-27-2016, 04:50 AM   #1
Location: US

Join Date: Jul 2013
Posts: 55
Default multifactor analysis or pairwise comparison?

I can't find a simple answer to what's the difference between doing multifactor analysis or pairwise comparisons, example:

I have two factors to consider: condition (treatment or control) and genotype (A and B). If I do
1. a pairwise comparison between control and treatment across both genotypes and
2. a pairwise comparison between treatment and control in genotype A and treatment and control in genotype B
I expect the intersection of these two pairwise comparisons to give the same results as if I do mutlifactor analysis taking into account both factors: condition and genotype (in DESeq2 something like design(ddsM) <- formula(~condition*genotype)) but I don't

What's in this case the biological interpretation of both analyses?
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