Entering edit mode
I am interested in the interaction between a stimulation of various cell lines and a specific genotype. I am particularly interested in the following contrasts:
- Differences between genotypes without stimulation (both Con HLA Pos vs Con HLA Neg and PDL HLA Pos vs PDL HLA Neg conditions)
- Differences between genotypes with stimulation (Fib HLA Pos vs Fib HLA Neg)
Therefore, I planned to run an interaction model like this:
form <- ~ 0 + HLA*Stim + (1 | ID)
However, I am stuck on how to setup contrasts for this more complex model. I'm sharing my metadata here for reference:
Any insight into the call I can make to makeContrastsDream for this interaction analysis? I looked at the examples provided online for making contrasts but didn't see an example with an interaction to follow.
gabriel.hoffman any insight?