What is FARMS

Readers shall find a quick introduction with recommendations into the preprocessing of Affymetrix GeneChip® microarrays. In the rapidly growing field of microarrays, gene expression, especially the Affymetrix GeneChip arrays, is an established technology present on the market for over ten years. Used in biomedical research, the mass of information demands statistics for its analysis. Here we present the particular design of GeneChip arrays, where much research has already been invested and some validation resources for the comparison of the methods are available. For a basic understanding of the preprocessing, we emphasize the steps, namely: background correction, normalization, perfect match correction, summarization, and couple these with alternative probe-gene assignments. Combined with a recommendation of successful methods a first use of the new technology becomes possible.