I've been having some trouble with getting my pipeline to execute what I want. Below is my ColData, and what I would like to look at is the following. First I would like to look at the main effect of treatment. I tried Design = Clone + Treatment and did a contrast of VPA vs Unt, but the results were way higher then they should've been, so something isn't right.
Then, I would like to look at the interaction effect, which I believe can be done with Design= Disease + Treatment, but I am not sure if I am executing things correctly, and I don't believe my resultsName(dds)- is showing me what I would like...but basically would like to look at SMS-VPA vs SMS-Unt, Cont-VPA vs Con-Unt etc etc
Any advice or help with be greatly appreciated
Clone Disease Treatment Age AT.1 A1 SMS VPA Y AT.2 A2 SMS VPA Y AT.3 A3 SMS VPA Y AU.1 A1 SMS Unt Y AU.2 A2 SMS Unt Y AU.3 A3 SMS Unt Y OT.1 O1 Con VPA Y OT.2 O2 Con VPA O OT.3 O3 Con VPA O OU.1 O1 Con Unt Y OU.2 O2 Con Unt O OU.3 O3 Con Unt O