I have an experimental design where I have 2 factors (A: 4 levels, B: 2 levels). I'm interested to look at both factor effects and its interaction. I'm having troubles understanding how to define the reduced model to run DEseq.
I define the full model as : A + B + A:B
My question is:
reduced model as: A+B means that I'm looking at DE genes of the interaction A:B?
reduced model as: A+A:B means that I'm looking at DE genes considering factor B?
reduced model as: B+A:B means that I'm looking at DE genes considering factor A?