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?
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:
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!
