[R] R factorial microarray analysis with a looped design

[meyer.ann]

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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