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