time course design matrix

Hi!

I'd welcome some help on creating a design matrix for a time-course experiment.

I have 7 time points (0,3,6,9,12,24,27 hours) with three technical
replicates at each time point. Cy3 is the untreated, Cy5 is the
treated sample on each chip. There is an example in the limma user
guide for time course experiments, but I'm still a bit confused about
design and contrast matrices.

Thanks in advance,

Endre Sebestyen

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