Question: DESeq2 Two-Factor Interaction Terms
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gravatar for bojingjia
2.8 years ago by
bojingjia10
United States
bojingjia10 wrote:

I am trying to understand the difference explored by interaction term for DESeq2. The vignette (p.38) explains that the interaction term answers: is the condition effect different across genotypes? There are two ways I think we can interpret this difference, and I'm wondering how to extract this information for the 2nd scenario.

For Condition X v Y || Genotype A v B:

1) Vignette's Definition of Difference: From what I've seen playing around with the code myself, the interaction term finds ie. a gene 123456 that is upregulated across X v Y for Genotype A but downregulated for X v Y for Genotype B. Is this understanding correct?

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2) Alternative Scenario of Interaction "Difference"

What I am interested in is a different scenario, wherein I want to identify genes that are let's say, unchanged for Genotype B but only upregulated across condition X v Y for Genotype A:

enter image description here

Is the 2nd scenario extracted by what the vignette calls "main effect plus the interaction term"? I'm not sure what that means either. Sorry if this is a naive question, and any help much appreciated!

rna-seq deseq2 • 1.1k views
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