[BioC] Limma time course with two-color microarrays

[Sergio Barberan]

Dear list,

It might be a really easy problem but I can not figure out how to do it.

I'm trying to analyze a set of hybs of a time course experiment, where I
used a loop design. I have six samples and no reference, I compare
(1-2,2-3,3-4,4-5,5-6,6-1); each with dye swaps so I have 12 slides.

By selecting sample 1 as my reference in modelMatrix, I get the following
design matrix:

 2 3 4 5 6
1      0 -1  1  0  0
2      0  0 -1  1  0
3      0  0  0 -1  1
4      1  0  0  0 -1
5      0  1  0  0  0
6      0  0  0  1 -1
7      0  1 -1  0  0
8     -1  0  0  0  1
9      1  0  0  0  0
10     0  0  1 -1  0
11     0 -1  0  0  0
12    -1  0  0  0  0

My question is: How to use contrastMatrix to obtain the following
comparisons: 1-2, 2-3, 3-4, 4-5, 5-6 and 6-1?
I know there is some information about Limma and time course experiments
but that example uses one-color arrays so I'm confused about how to apply
that to my experimental design.

Thanks in advance for any help,
Sergio