Hi, I have a 2*2 factorial experiment. w1: wildtype without treatment w2: wildtype with treatment m1: mutant without treatment m2: mutant with treatment w1--->w2 and dye-swap m1--->m2 and dye-swap w1--->m1 and dye-swap w2--->m2 and dye-swap w1--->m2 m1--->w2 total ten slides factor a is strain, and b is treatment. my design matrix is a b ab w1--->w2 0 1 0 w1<---w2 0 -1 0 m1--->m2 0 1 1 m1<---m2 0 -1 -1 w1--->m1 1 0 0 w1<---m1 -1 0 0 w2--->m2 1 0 1 w2<---m2 -1 0 -1 w1--->m2 1 1 1 m1--->w2 -1 1 0 I want to make comparisons w2 vs w1, m2 vs m1, m1 vs w1, and m2 vs w2 by using makeContrasts(), so I did like following contrast.matrix<-makeContrasts(W2vsW1=b,M2vsM1=b+ab,M2vsW2=a+ab,M1vsW1 =a,levels=design) but I am not sure that my contrast matrix is correct or not. Could anyone tell me it is correct? Thanks for any help. Ren [[alternative HTML version deleted]]