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The Detection of Blur in Affymetrix GeneChips

Author

Listed:
  • Upton Graham J. G.

    (University of Essex)

  • Harrison Andrew P

    (University of Essex)

Abstract

High correlations were obtained between probes in seemingly unrelated probe sets, following an examination of the data from thousands of Affymetrix GeneChips. Investigation revealed that these unexpected correlations were between probes that were adjacent to high-valued probes. Using carefully selected probes, together with simple linear models, the extent of blur has been measured for each CEL file. The cause is shown to be attributable to poorly performing scanners. Blur can result in the doubling of the values of thousands of probes. This in turn can lead to the doubling of the expression level for hundreds of probe sets.

Suggested Citation

  • Upton Graham J. G. & Harrison Andrew P, 2010. "The Detection of Blur in Affymetrix GeneChips," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-19, October.
    • Handle: RePEc:bpj:sagmbi:v:9:y:2010:i:1:n:37
    DOI: 10.2202/1544-6115.1590
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    References listed on IDEAS

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    1. Zhijin Wu & Rafael Irizarry & Robert Gentleman & Francisco Martinez Murillo & Forrest Spencer, 2004. "A Model Based Background Adjustment for Oligonucleotide Expression Arrays," Johns Hopkins University Dept. of Biostatistics Working Paper Series 1001, Berkeley Electronic Press.
    2. Zhijin Wu & Rafael A. Irizarry & Robert Gentleman & Francisco Martinez-Murillo & Forrest Spencer, 2004. "A Model-Based Background Adjustment for Oligonucleotide Expression Arrays," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 909-917, December.
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