I am new to microarray analysis and need help on two fronts:

1. Can any one direct me to a resources that provide directions on a how to systematically conduct an analysis of differential expression data. 

Something like what the paper by Harrel and others "Tutorial in biostatistics,
multivariate prognostic models: issues in developing models, evaluating
assumptions and adequacy, and measuring and reducing errors" provides for regular biostatistical analysis

2. I have this affymetrix hg_u1332a chip data in a 22000 X 62 matrix. The columns are different patients and I am seeking suggestions on analysis. My goal is to report on informative genes relative to disease under study.

Thanks for all the help I can get.
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