I am reading through the DESeq2 manual and saw the different examples in the results help page. I have a couple of questions to make sure I am understanding these things properly. I am focused more on "Example 3: two conditions, three sets".
1. If I wanted to compare the set Z effect to that of set X, (instead of the average of X and Y as stated in the example), I think either of the following command should work:
results(dds, contrast=list("setZ","setX")) or results(dds, contrast=c("set","Z","X"))
and this should capture the effect of Z compared to X irrespective of the condition, correct?
2. If I want to test set Z vs. X effect for conditionB, I could just use the combination of variables and compare "ZB" and "XB", correct? But if I want to do the same using an interaction design, would the command be:
results(dds, contrast=list(c("setZ", "setZ.conditionB"),c("setX", "setX.conditionB")))
3. This is more about just the idea of interacting terms, why does the log2 fold change of some genes change drastically when comparing results from a design with interaction to the results from a design without interaction? For example, if I just look at the main effect for condition then I see certain genes with very different fold change values between the two designs. Is this due to the additive nature of interacting terms, if not then what does such an observation represent?
I have read the manual and several other posts on deseq2 designs and contrasts before posting these questions. I apologize in advance some of these things are redundant questions that have already been answered and I missed them. Any insights on the above questions will be very helpful :)