Hi, I have Affymetrix gene chip data from time course experiment with 2 different cell lines, 4 time points ("day0", "day7", "day14", "day21"), 2 replicates at each time. I want to "normalize" each probe at times "day7", "day14", "day21" on its expression at time "day0"; following step would be the use of linear models to identify D.E. probes in cell line A vs cell line B at each time point. Any idea on how to perform this analysis? Do you know if I can manage eset objects in limma package in this way? Thank you in advance, Andrea Dr. Andrea Grilli andrea.grilli at ior.it phone 051/63.66.756 Laboratory of Experimental Oncology Rizzoli Orthopaedic Institute Codivilla Putti Research Center via di Barbiano 1/10 40136 - Bologna - Italy

Hi, I have Affymetrix gene chip data from time course experiment with 2 different cell lines, 4 time points ("day0", "day7", "day14", "day21"), 2 replicates at each time. I want to "normalize" each probe at times "day7", "day14", "day21" on its expression at time "day0"; following step would be the use of linear models to identify D.E. probes in cell line A vs cell line B at each time point. Any idea on how to perform this analysis? Do you know if I can manage eset objects in limma package in this way? Thank you in advance, Andrea Dr. Andrea Grilli andrea.grilli at ior.it phone 051/63.66.756 Laboratory of Experimental Oncology Rizzoli Orthopaedic Institute Codivilla Putti Research Center via di Barbiano 1/10 40136 - Bologna - Italy