Hi all, I would like to run a GLM using Limma, I have 3 coffecients

 biopsy met resect        
1       1   0      0  
2       1   0      0  
3       1   0      0  
4       1   0      0 
5       1   0      0 
6       0   0      1 
7       0   0      1  
8       0   1      0 
9       0   1      0 
10      0   1      0  

so for my contrast I want to compare (1) biopsy vs. resect (2) biopsy vs. met, however I would also like to (3) combine resect with met vs. biopsy.  

my contrast looks like this, 

cont.mod <- makeContrasts(MB=met-biopsy,RB=resect-biopsy,levels=design)

however if I wanted to combine resect with met (treating it as one group) vs. biopsy is this the correct way to approach it? 

thank you!

cont.mod <- makeContrasts(MB=met-biopsy,RB=resect-biopsy,MRB=(met+biopsy)/2-biopsy, levels=design)

First a pedantic note. limma doesn't fit a glm, it fits a conventional linear model.

Your contrast isn't correct, probably just because of a typo. What you really want is

cont.mod <- makeContrasts(MB=met-biopsy,RB=resect-biopsy,MRB=(met+resect)/2-biopsy, levels=design)

Which will test that the mean of met and resect is different from biopsy.