Hello all, I would like to create a linear model where i have 4 tissues, 2 types of mice and 3 time points. I created the following data frame: Type Tissue Time Value Ty1 Tis1 T1 V1 Ty2 Tis1 T1 V2 ... For each Type Tissue and Time point i have 3 replicates. I need to create a model like Y ~ Type x Tissue x Time and calculate the contrasts (all possible combinations). I need some help on the way i can use limma to do something like the above. For example something like: design = model.matrix (~ Data$Type x Data$Tissue x Data$Time) would it work? How can i take all the possible contrasts? thanks in advance, Dimitris [[alternative HTML version deleted]]