[BioC] limma design matrix for two color arrays with common reference

[zones]

Hello,

I am confused about how my design matrix should look.  I have data  
from 14 arrays, each with the same common reference in one channel  
and a sample of interest in the other.  There are technical and  
biological replicates of each sample with wild type and two different  
mutants as follows:

#		green	red
1		ref		wt-A
2		ref		wt-A
3		ref		wt-B
4		ref		wt-B
5		ref		wt-C
6		ref		wt-C
7		ref		mut1-A
8		ref		mut1-A
9		ref		mut1-B
10		ref		mut1-B
11		ref		mut2-A
12		ref		mut2-A
13		ref		mut2-B
14		ref		mut2-B

I wish to use duplicateCorrelation for the replicate arrays and then  
ask what genes are differentially expressed in each mutant relative  
to wild type.  Any help is appreciated.

Thanks in advance!

Matt