[BioC] Limma time series analysis question

[January Weiner]

Dear all,

I am wondering what would be the optimal approach for limma to the
following setup:

I have an experiment repeated three times (A, B, C). Each repeat is
measured at five different time points (T1...T5) in three replicates
(R1...R3):

A T1 R1
A T1 R2
A T1 R3
A T2 R1
...

C T5 R1
C T5 R2
C T5 R3

Thus, A T1 is matched with A T2, T3, T4 and T5, but not with the B
series. So it is a mixed design.

I want to see genes that are differentially expressed relative to T1.
How do I do it correctly in limma?

Best regards,
j.

-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web   : www.mpiib-berlin.mpg.de
Tel     : +49-30-28460514