There was an earlier post that nicely explained how to build a design matrix for a paired responder vs non-repsonder analysis: https://support.bioconductor.org/p/95143/#124666
In that example, the assumption was that there were two conditions, "screen" and "treatment", representing before and after treatment. What if instead there are several conditions, say "before", "during" and "after", how would you specify that you want "before" to be the base case for your comparison to "during" or "after"? It seems like it might be defaulting to alphabetical order, leaving me without the "groupY.conditionAfter" and "groupN.conditionAfter" variables to contrast.
I also commented in that other post if anyone prefers to respond there. Thanks!