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".)

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


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