[BioC] Help: longitudinal data

[Narinder Singh Sahni]

Hello All,

We are two students doing a project which involves analyzing
time-course experiments. There are two strains of entamoeba histolytica 
hybridised using Affy. measured at three different time points.

We have two questions that would at-least get us started:
1) What are the best measures of filtering genes in time-course experiments.
Some of the genes have been replicated.

2) What would be the most recommended techniques to focus on
for such a sparse data set.

Thanking all for their assistance.

Aftab & Aditi