Quality Assessment of Affymetrix GeneChip Data

  • B. M. Bolstad
  • F. Collin
  • J. Brettschneider
  • K. Simpson
  • L. Cope
  • R. A. Irizarry
  • T.P. Speed
Part of the Statistics for Biology and Health book series (SBH)

Abstract

This chapter covers quality assessment for Affymetrix GeneChip data. The focus is on procedures available from the affy and affy-PLM packages. Initially some exploratory plots provided by the affy package, including images of the raw probe-level data, boxplots, histograms, and M vs A plots are examined. Next methods for assessing RNA degradation are discussed, specifically we compare the standard procedures recommended by Affymetrix and RNA degradation plots. Finally, we investigate how appropriate probe-level models yield good quality assessment tools. Chip pseudo-images of residuals and weights obtained from fitting robust linear models to the probe level data can be used as a visual tool for identifying artifacts on GeneChip microarrays. Other output from the probe-level modeling tools provide summary plots that may be used to identify aberrant chips.

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • B. M. Bolstad
  • F. Collin
  • J. Brettschneider
  • K. Simpson
  • L. Cope
  • R. A. Irizarry
  • T.P. Speed

There are no affiliations available

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