[BioC] LIMMA question

[Richardson, Dawn K]

Dear All,

My experimental set up is as follows:

Time course experiment in 10 subjects each given treatment for 240
minutes.  

During the course of the treatment I took a muscle biopsy at time 0, 30
and 240 min. I extracted RNA from the biopsies at all time points and
used the Affymetrix HG-U133A chips for each sample.

I normalized all CEL files together using GC-RMA and I'm at the stage
where I want to look for genes that are differentially expressed at all
time points; i.e. time 0 versus time 30, time 0 versus time 240, and
time 30 versus 240.

I have looked in the LIMMA manual and I'm not sure which script I need
to use to perform this test.  

Any help or suggestions would be appreciated,

Thanks,

Dawn.