Dear all, I am wondering what would be the optimal approach for limma to the following setup: I have an experiment repeated three times (A, B, C). Each repeat is measured at five different time points (T1...T5) in three replicates (R1...R3): A T1 R1 A T1 R2 A T1 R3 A T2 R1 ... C T5 R1 C T5 R2 C T5 R3 Thus, A T1 is matched with A T2, T3, T4 and T5, but not with the B series. So it is a mixed design. I want to see genes that are differentially expressed relative to T1. How do I do it correctly in limma? Best regards, j. -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514