I have the following design matrix:
mm_noreps.interactions <- model.matrix(~condition*TRAPed)
Both variables are factors condition has 4 levels and TRAPed has 2 levels.
I want to use the following contrasts:
- TRAP positive (just consider this a drug treatment) vs TRAP negative in all conditions, c(-1,0,0,0,0,1,0,0)
- FearRecallpositive vs all other condition's positive cells c(0,0,-1/3,0,-1/3,-1/3,0,1), and
- FearRecallpostive vs all other conditions c(-1/7,-1/7,-1/7,-1/7,-1/7,-1/7,-1/7,1).
The main question I have is are there differentially expressed genes specific to the FearRecall:TRAPedpostive interaction. Does contrast 3 address this? The other two are more sanity checks than actual contrasts of interest.