Processing Affymetrix Expression Data

  • R. Gentleman
  • W. Huber
Part of the Use R! book series (USE R)


In this chapter we do an analysis of Affymetrix gene expression data. We begin with the CEL files that contain the raw microarray readings, discuss how to do quality assessment, and proceed to normalization and the estimation of expression values. Finally, we determine differentially expressed genes.


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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  1. 1.Division of Public Health Sciences, Program in Computational BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Wellcome Trust Genome CampusEuropean Bioinformatics Institute, EMBL Outstation HinxtonCambridgeUK

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