[BioC] limma 2*2 factorial design contrast matrix

Na, Ren Na at uthscsa.edu
Thu Dec 9 21:28:27 CET 2004


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
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
but I am not sure that my contrast matrix is correct or not. Could anyone tell me it is correct?

Thanks for any help.


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