Dear All, I have a time series data from two different samples (treatment A and treatment B) at 3 different time points (0 hr, 6 hr and 24 hr) , the control is time = 0 hr. Both datasets have three replicates. I have already analyzed these data using limma, just to have an idea of regulated genes at 6 hr and 24 hr, but now I would like to cluster the data across the time points to group the genes according to their expression profile. My question is: what method should I use in order to do this? I have checked already the timecourse<http: www.bioconductor.org="" packages="" release="" bi="" oc="" html="" timecourse.html="">package, but I'm afraid it includes a different method for defining differentially expressed genes (and I would like to be consistent with limma's results). Any clue? I will really appreciate any help from you. Thank you! Avhena [[alternative HTML version deleted]]