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

[Federico Scossa]

Hi all !
I posted a message several days ago but I didn't get any answers. So I 
assume that the time effect in a direct comparison exp. design (across 
multiple timepoints) is non-estimable.
Is there anyone able to confirm my assumption?

I paste my old message again here:

"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."

Any comment or suggestion is really appreciated.
Thank you.
Federico