interaction term formula for DESEQ2?
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@183232d3
Last seen 10 hours ago
Czechia

Hi all,

I have a situation like WT, KO, WT+DRUG, KO+DRUG (5 replicates each). The initial idea to do the pair wise comparison and i did it. I have the results for WT vs KO and WT+DRUG, vs KO+DRUG. But i would like to run DESEQ2 with interaction term. would it be vice if i consider WT vs KO as genotype-1 and WT+DRUG, vs KO+DRUG as a genotype-2. And my formula is

design(dds) <- ~ genotype + condition + genotype:condition

Or do i have to change.

DESeq2 • 92 views
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swbarnes2 ★ 1.1k
@swbarnes2-14086
Last seen 2 hours ago
San Diego

With the right results call, this should return what you want.

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