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Processing and Analyzing Affymetrix SNP Chips with Bioconductor

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Abstract

We briefly review some principles of the Bioconductor project for statistical analysis of genome scale data and show in detail how these are deployed to analyze high-density genotyping arrays manufactured by Affymetrix, Inc. (Genome-wide SNP 6.0). Issues addressed include probe design and verification of probe address assertions, preprocessing of scanned intensities via SNPRMA, genotype calling via CRLMM, and downstream analysis of genotype-expression associations.

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Authors and Affiliations

  1. Johns Hopkins University, Baltimore, MD, USA

    Benilton Carvalho, Rafael A. Irizarry & Robert B. Scharpf

  2. Harvard University, Cambridge, MA, USA

    Vincent J. Carey

Authors
  1. Benilton Carvalho
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  2. Rafael A. Irizarry
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  3. Robert B. Scharpf
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  4. Vincent J. Carey
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Corresponding author

Correspondence to Vincent J. Carey.

Additional information

Work supported in part by NIH P41 HG004059-01 and NIH R01 HL086601-01.

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Carvalho, B., Irizarry, R.A., Scharpf, R.B. et al. Processing and Analyzing Affymetrix SNP Chips with Bioconductor. Stat Biosci 1, 160–180 (2009). https://doi.org/10.1007/s12561-009-9015-0

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  • DOI: https://doi.org/10.1007/s12561-009-9015-0

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