[BioC] LIMMA - timecourse and direct comparison exp. design

[Federico Scossa]

Hi all,
my experiment is a 2-color direct comparison wt vs mutant, but repeated on 
5 successive timepoints.
each timepoint is structured this way:

FileName	Cy3	Cy5
1		mu1	wt1
2		wt1	mu1
3		mu2	 wt2
4		wt2	mu2

(1 and 2 are to distinguish the 2 bioreps)

I'm interested not only in the DE genes between wt and mutant at each 
timepoint, but I would like to extract information independently from the 
wt and mutant time-courses, even if I don't have direct comparison between 
successive timepoints. Is this possible? I think there is an example in 
limma's user guide (chapter 16, time-course experiments), but it is for 
one-color array (at least, I guess), and I don't really know how to adapt 
the script to my case.
Can anyone point me in the right direction? (please forgive my lack of 
statistical knowledge!)
Thank you.
Federico