[BioC] Contrast matrix in limma

[kaushal Chaudhary [guest]]

Hello,

In my micro array expriemt,  I have  four different types of  samples (nodiet.nodisease, nodiet.disease, diet.nodisease, and diet.disease).  I want to make the  following 5 comparisons.
Diet.nodisease vs.  nodiet.nodisease (effect of diet  in no disease)
Diet.disease vs. nodiet.disease  (effect of diet in disease)
Nodiet.disease vs. Nodiet.nodiease (effect of disease in no diet)
Diet.disease vs. Diet.nodisease (effect of disease in diet)
Diet.disease vs. nodiet.nodisease 
I used  makecontrasts function  in limma in R.
Contrast.matrix=makecontrasts(
                                                 Diet.nodisease vs.  nodiet.nodisease= Diet.nodisease - nodiet.nodisease
                                                  Diet.disease vs. nodiet.disease  = Diet.disease - nodiet.disease  
                                                  Nodiet.disease vs. Nodiet.nodiease= Nodiet.disease -Nodiet.nodiease  
                                                  Diet.disease vs. Diet.nodisease= Diet.disease - Diet.nodisease 
                                                 Diet.disease vs. nodiet.nodisease= Diet.disease -  nodiet.nodisease 
                                                  )

I also want to get the main effect of diet and disease and interaction at  the same time. (diet, disease, diet*disease).  I suppose the code gives  2 diet effects and 2 diseases effect.   I would appreciate any advice. 
 
Thanks !!!



 -- output of sessionInfo(): 

None.

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