On the causes of outliers in Affymetrix GeneChip data

Brief Funct Genomic Proteomic. 2009 May;8(3):199-212. doi: 10.1093/bfgp/elp027.

Abstract

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Artifacts*
  • Base Sequence
  • DNA Probes / metabolism
  • Humans
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data*
  • Statistics as Topic

Substances

  • DNA Probes