What have you tried so far, and where, exactly, does the uncertainty lie? Generally, people like to see that you have invested some effort before posting a question in an online forum like this. That's because we invest effort in providing answers. There are countless examples across the World Wide Web of how to process Affymetrix microarray data, including how to construct the design matrix. There is also the limma manual pages. Edit: for Affymetrix array pre-processing, take a look at oligo and affy packages.