[BioC] short time-course design. Any suggestion?

[Stefano Calza]

Hi everybody.

I'm looking at a small experiment with 12 chips (Affy), from 3 different cell lines measured at 4 different time points (0,2 hours, 8 h, 24 h).

1) mas5 expression values
2) selected about 1500 genes (out of ~22000) using GO annotations for those BP of possible interest
3) selected genes with at least 25% Presence/Calls (I know this is quite arbitrary).
4) ANOVA using gls with Compound Symmetry correlation structure
5) p value corrected either using p.adjust(...,"fdr") or computing Q values.

I actually get few "significant" genes and mostly with low fold-change (relative to time 0) and overall low expression intensities.
Any objection about all this and/or any suggestion for improvement? 

Thanks in advance,
Ste