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Hi I have not understood very well how to realize, in limma package, the design (using factor in model.matrix) to insert in lmFit. I have an experiment with 4 groups (a,b,c,d) with 3 replicates for each-one and i have to compare a vs b; c vs d; ( a&c )vs (b&d). List Sample in pdata is like this: 1a 1c 1b 1d 2a 2c 2b 2d 3a 3c 3b 3d How can i do this design with matrix model? thanks