Producing a useful list of differentially expressed genes from microarray data sounds like an easy task. However, our experience is different. Being caught in various traps ourselves, we will warn of the most dangerous pitfalls. Some 'roads to the list' are relatively safe to travel on, and we will point them out. The trip usually splits into two parts, and can be stopped after the first. At the beginning is explorative analysis which leads to candidate genes. Having arrived at this destination, you can transit to statistical analysis. This leads to quality measures, and allows you to distinguish between a reliable result and an unreliable one.

You can choose almost every generic statistical software for analysis. We recommend using the open source language R (1) together with the bio-informatics R-packages collected by the Bioconductor project (2). R is freely available at, and Bioconductor at http://www. Throughout the chapter we will give you precise information for your 'trip to the gene list using R'.

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