[BioC] limma - Identifying interactions

[James W. MacDonald]

Hi Suzanne,

Suzanne Szak wrote:
> Hi all,
> 
> I'd like to use limma to identify a possible interaction between two drugs 
> (called "x" and "y") which would be reflected in gene expression.  That 
> is, each drug has its own effect, but I think there might be synergy 
> between the two drugs if cells are treated with both of them ("combo").
> 
> What should the design matrix and contrast matrix look like?  I tried the 
> matrices below (as well as other variations) without any luck.  And, given 
> the correct design and contrast matrices, how do I interpret the results 
> to get the answer I want?  (e.g. I want to find genes in which "combo" > 
> "x" + "y".)

What do you mean by 'without any luck'? The fourth contrast below should 
give you what you want (Combo - x - y + control).

Best,

Jim


> 
> Thanks much,
> Suzanne
> 
>> design
>                         x       y       Combo           Control
> x.cel                   1       0       0               1
> x.cel                   1       0       0               1
> y.cel                   0       1       0               1
> y.cel                   0       1       0               1
> control.cel             0       0       0               1
> control.cel             0       0       0               1
> combo.cel               1       1       1               1
> combo.cel               1       1       1               1
> 
> 
>> contrast.matrix
> 
>         combo-control   x-control       y-control 
> x                       0               1               0
> y                       0               0               1
> combo                   1               0               0
> control         -1              -1              -1
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826