Bioconductor comunity: I have been trying to find the best way to answer the classical questions for a timeseries with two treatment effect. Altough I have been reading I am not able to find an example about the best matrix design and contrasts in order to answer the above questions. If I use modelMatrix() using the targets frame I have got a matrix design that makes me able to identify genes with differential expression between treatments in a single time point. But about the second question, how the treatment changes across the timeseries? I'm not sure how to treat it. I guess that I need to analyze the interaction between time and treatment but my so poor experience using linear models and making contrasts limits my analysis, so I think I am not fully taking advantage of all the data. The experiment is a two-color time series experiment, 4 time points, 2 treatments, 16 arrays: t1--->t2--->t3--->t4--->t1 II II II II c4<---c1<---c2<---c3<---c4 2hybs per time point for direct comparisons (getting 8 slides) plus the other 8 slides to make hybs across times, as indicated in the representation. Thank you in advance.