Hi Prof. Gordon Smyth,
I have a question about the meaning of interaction terms in design matrix on the page 38 in the edgeR User's Guide. In line 19, the guide say: "The last two coefficients give the DrugvsPlacebo.1h and DrugvsPlacebo.2h contrasts". But my understanding is that the last two coefficients (  "TreatDrug:Time1h",  "TreatDrug:Time2h" in model.matrix(~Treat * Time, data=targets)) could be the difference of difference, which means the effects (Drug.1h-placbo.1h)-(Drug.0h-placebo.0h) and (Drug.2h-placbo.2h)-(Drug.0h-placebo.0h). (Drug.0h-placebo.0h) is the reference level for interaction. Is my understanding right?
Best, Mingxing Yang