Hi

I have some problems making my contrast matrix. 

I have the following design matrix:
	P_s	P_us	D_s	D_us
S1	1	0	0	0
S2	1	0	0	0	
S3	0	1	0	0
S4	0	1	0	0
S5	0	0	1	0
S6	0	0	1	0	
S7	0	0	0	1
S8	0	0	0	1


Where P = patiens and D = donor, s = stimulated and us = unstimulated

What I want is to find the following differences:
The differences between stimulated and unstimulated in the patients group, and the differences between stimulated and unstimulated in the donor group. This I am able to make, the two first contrasts.

But then I also want to see the difference between the two treatmens undepended of samples: stimulated vs unstimulated. 
In other words: (P_s and D_s) vs (P_us and D_us). Is my last contrast correct or should I do something else?
                                                                        
contrast.matrix <- 
makeContrasts(P_s-P_us, D_s-D_us, (P_s-P_us + D_s-D_us)/4, levels = designMa)                                  

Regards,
Ingrid




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