Gene discovery in neuropharmacological and behavioral studies using Affymetrix microarray data

We describe methods and software tools for doing data analysis based on Affymetrix microarray data, emphasizing often neglected issues. In our experience with neuroscience studies, experimental design and quality assessment are vital. We also describe in detail the pre-processing methods we have found useful for Affymetrix data. Finally, we summarize the statistical literature and describe some pitfalls in the post-processing analysis.