Dear BioC members, I have a general question on analysis of complicated designed microarray experiment.The experiment is designed as follows: Factors interested: 1. Cell Type: WT, MU1, MU2, MU3 2. Treatment: Hormone and Untreated Each combination of treatment was repeated twice and hybridized to Affy genechip. Because the experiment is time-consuming, two technicians will do the experiments at two different time. Extraneous factors not interested: 1. Day: two lelves 2. Experimenter: two levels Correct me if I am wrong: If the experimter and day is combined, it is a randomized block design. Otherwise, it will be a latin square deisgn. We are only interested in the cell type difference and treatment difference or their interaction, but not day or technician effect. I think this situation could be quite common in practice. My question is : 1) Is there a package helping design such experiment? 2) Is there a way to analyze the data using Limma packages or other R packages? Any input will be highly appreciated, Xiwei Wu, MD, PhD Assistant Research Scientist Department of Biomedical Informatics Beckman Research Insitute City of Hope National Medical Center Duarte, CA 91010 Phone: (626) 359-8111 ext. 65071 "EMF <coh.org>" made the following annotations. ---------------------------------------------------------------------- -------- SECURITY/CONFIDENTIALITY WARNING: This message and any atta...{{dropped}}