Hello All! I am hoping that someone might have some suggestions for a normalization method when some of the samples in an experiment are very divergent due to biology, not artifact. I have tried out several (loess, rma, vsn, quantile) but I am worried by how similar the distributions look afterwards. It would be best to use a set of 'housekeeping genes'? The normal ones (rRNA, gapdh, actin, etc) all are biologically different in these treatments too (think dying tissue). Formally we were using mas5 type summarization......but since it isn't the most robust I wanted to try some other methods out. Is the mas5 type of constant normalization really the best for this type of data and I am chasing my tail? Thanks for any advice! Siobhan S. A. Braybrook Graduate Student, Harada Lab Section of Plant Biology University of California, Davis Davis, CA 95616 Ph 530.752.6980 The time is always right, to do what is right. - Martin Luther King, Jr. [[alternative HTML version deleted]]