Hi everyone, I know my question is answered in some extent on mail list. But I am still not feel very confidence about my design. I really appreciate if anyone can help me on this. the data set is about the patients before and after treatment. for example, for 3 patients. I want to find out the genes that changed expression before and after treatment. if I have 3 patients, I did like this: >design patient1 patient2 patient3 treatment14 1 1 0 0 0 2 0 1 0 0 3 0 0 1 0 4 1 0 0 1 5 0 1 0 1 6 0 0 1 1 attr(,"assign") [1] 1 1 1 2 attr(,"contrasts") attr(,"contrasts")$patient [1] "contr.treatment" attr(,"contrasts")$treatment [1] "contr.treatment" >eset.rma.fit = lmFit(eset.rma, design); >eset.rma.bayes = eBayes(eset.rma.fit); >topTable(eset4.rma.bayes, coef = "treatment14", adjust = "BH"); thank you very much. Wenhuo Hu ===================================================================== Please note that this e-mail and any files transmitted with it may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.