Contrast matrix for paired samples in limma

Question

[ddzhangzz]

I would ask a question for analysis of paired sample in limma. Suppose I have a manifest file such like this:

   id group
    1 A
    1 B
    1 C
    2 A
    2 B
    2 C
    3 A
    3 B
    3 C

My question is what a correct design and contrast matrix for a paired comparison between A vs B will look like if I were using limma package.

[michael.r.dufault]

I am also interested in this same setup. It appears to be similar to a paired t-test example. Can anyone comment as to what the correct setup would be? Thanks.