Hi, I need help with analysis using the limma package. Here is the experiment design: 20 patients, 10 on a regular diet and the other 10 on a special treatment diet. For each patient, 4 samples were obtained: day 1, before and after diet; day 6, before and after diet. Thus there are a total of 20x4=80 arrays. And the purpose of the study is to find out the effect of the treatment diet. Here the treatment is nested with the patient (if that's the right way to say it). It can be viewed as a paired analysis but the pair is for both before/after treatment and day1/day6. I am at lost as how to create a design matrix and call limma for such a study design. Can someone please help? Any input will be highly appreciated! Yiwen He BIMAS/CIT/NIH