Hello!

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)
    [1] "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!
I found this website helpful in working out the right way to deal with interactions

https://rpubs.com/ge600/deseq2

I think you likely want "conditionko.experimentyoung", or what's likely more useful is to relevel age so that young is the control, and then the contrast will be "conditionko.experimentadult"