[BioC] limma - paired design

[Mayra Eduardoff]

Hi,
I am having problems fitting the following model into limma, I have
tried many different ways of specifying the design and contrast matrix
but they all seem nonsense so I won t post them here, but maybe anyone
knows how to properly fit this:

I have data from 13 Patients, sampled at three different time points,
0h (Control), 6h Treatment, 24h Treatment, so all in all 39 arrays and
I want to do paired t tests for differential expression between 6h-0h
and 24h-0h (not ! an ANOVA over both Time points). Until now we have
been doing this fitting the model for the 6h and 24h separately, which
works fine, but in oder to take all data into account for the mod. t
tests variance estimator I guess i need to fit all data into one
model.

kind regards,

Mayra