> we have recently finished a large microarray experiment on
> HGU133plus2 (each experimental point is in triplicate) made of 4
> different compound treatments on the same cell line investigated at
> 0, 1,2,3,4,5,6,24 hours.
We have had good experience with the maSigPro package for timecourse
investigation, I encourage you to check it out. You should be able to
include the "day effect" as an additional factor to assess the
significance and any correlations with your treatment factors.
The "timecourse" package does not seem to have this ability, and worse
(for us), it only provides relative rankings, not significance
testing.
-Aaron
