Quality Assessment of Affymetrix GeneChip Data

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.