Processing and analyzing Affymetrix SNP chips with Bioconductor

Benilton Carvalho, Rafael A. Irizarry, Robert B. Scharpf, Vincent J. Carey

Research output: Contribution to journalReview articlepeer-review

3 Scopus citations


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. (Genomewide 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.

Original languageEnglish (US)
Pages (from-to)160-180
Number of pages21
JournalStatistics in Biosciences
Issue number2
StatePublished - 2009


  • Genetic epidemiology
  • Genetics of gene expression
  • Statistical analysis of microarrays

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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