Dear List, I need help with the analysis of time series experiment. I have cDNA microarray data produced with genepix. Bacterial cells were induced for sporulation (3 biological replicates), RNA was extracted from cells before induction and after 1,2,3 and 4 hours after induction. RNA from uninduced cells was labeled with Cy3, from respective induced cells with Cy5 and hybriduzed onto two-color microarray. To summarize the data: # biol repl Cy5 Cy3 3 1h unind 3 2h unind 3 3h unind 3 4h unind How should I analyze this data to find differentially expressed genes? I am trying to use limma package, but I cannot come up with proper design matrix to fit the linear model. I will very much appreciate any help, as I am not very experienced microarray data analyst. Thank to everyone, Olga. [[alternative HTML version deleted]]