I'm super noob on DESeq interactions so sorry in advance if this question is duplicated. I just need to ask directly to see if I understand correctly.
I have two experiments performed in young and old mice. I want to test in both for knock down vs control of a certain gene. I want to make a differential expression analysis between conditions (ko vs ctrl) and between experiments (young vs old).
My coldata looks like
sample condition experiment mouse1 ctrl young mouse2 ctrl young mouse3 ctrl young mouse4 ko young mouse5 ko young mouse6 ko young mouse7 ctrl adult mouse8 ctrl adult mouse9 ctrl adult mouse10 ko adult mouse11 ko adult mouse12 ko adult
But I am not really interested on what are all the differences between young and old mice, but only those that have an impact on the ko vs ctrl test.
So my design for the DESeq object is ~ condition + experiment + condition:experiment
> resultsNames(dds)  "Intercept" "condition_ko_vs_ctrl" "experiment_young_vs_adult" "conditionko.experimentyoung"
I am not sure, but the intuitive thing to do would be to take experiment_young_vs_adult. Is this correct?
Also, could someone explain why do I not have "conditionko.experimentadult", "conditionctrl.experimentadult", "conditionko.experimentyoung" in resultsNames(dds)?
Thank you in advance!