Treating 2 coefficients as the same group in Limma
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Ahdee ▴ 50
@ahdee-8938
Last seen 16 days ago
United States

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)

 

 

limma glm • 564 views
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@james-w-macdonald-5106
Last seen 12 hours ago
United States

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.

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cool thanks; also in case someone is reading this for reference, soon after I tested this out by creating a different design with a merge coeffecients: the results were the same.  Aha, yes typo, thanks. 

 

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