Hi. How do I set up a design and contrast matrix for the following experiment. I have unstimulated cells and stimulated cells for individuals with and without disease. sample groups 1 Disease Unstimulated 2 Disease Stimulated 3 No Disease Unstimulated 4 No Disease Stimulated Although I can set up design matrix for all two way comparisons, I am really interested in what genes are different between disease and no disease after stimulation of the cells. I could take ratios of Unstimulated/stimulated chip data for disease and no disease then have only two groups but I am not sure if this is optimal. ie new sample groups 1 Disease Stimulated/Unstimulated 2 No Disease Stimulated/Unstimulated Any advice gratefully received. Anthony -- ______________________________________________ Anthony Bosco - PhD Student Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au