Hi
I'm using the Limma package to analyze microarray data from a 2x2 factorial
loop design.
u --- t
l l
l l
v --- v.t
The samples hybridized to my arrays are: u/t, t/v.t, v.t/t, v.t/v, v/u, and
u/v.
My design matrix is:
v t v.t
v 1 0 0
t 0 1 0
v+v.t 1 0 1
-t-v.t 0 -1 -1
-v -1 0 0
-v-v.t -1 0 -1
I need to find the main effect t, the main effect v, and the interaction
effect v.t and have tried several different contrast matrices but none have
worked so far since I need to separate t and v from the arrays with v.t on
them (and vice versa).
Any help would be appreciated.
(The array design and design matrix are from Nature Reviews Genetics 3,
579-588 (August 2002) | doi:10.1038/nrg863 by Yang and Speed.)
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