Processing and analyzing Affymetrix SNP chips with Bioconductor

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

doi:10.1007/s12561-009-9015-0

Processing and analyzing Affymetrix SNP chips with Bioconductor

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

School of Medicine

Research output: Contribution to journal › Review article › peer-review

3 Scopus citations

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. (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 language	English (US)
Pages (from-to)	160-180
Number of pages	21
Journal	Statistics in Biosciences
Volume	1
Issue number	2
DOIs	https://doi.org/10.1007/s12561-009-9015-0
State	Published - 2009

Keywords

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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10.1007/s12561-009-9015-0

Cite this

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title = "Processing and analyzing Affymetrix SNP chips with Bioconductor",

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. (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.",

keywords = "Genetic epidemiology, Genetics of gene expression, Statistical analysis of microarrays",

author = "Benilton Carvalho and Irizarry, {Rafael A.} and Scharpf, {Robert B.} and Carey, {Vincent J.}",

note = "Funding Information: Work supported in part by NIH P41 HG004059-01 and NIH R01 HL086601-01.",

year = "2009",

doi = "10.1007/s12561-009-9015-0",

language = "English (US)",

volume = "1",

pages = "160--180",

journal = "Statistics in Biosciences",

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T1 - Processing and analyzing Affymetrix SNP chips with Bioconductor

AU - Carvalho, Benilton

AU - Irizarry, Rafael A.

AU - Scharpf, Robert B.

AU - Carey, Vincent J.

N1 - Funding Information: Work supported in part by NIH P41 HG004059-01 and NIH R01 HL086601-01.

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

KW - Genetic epidemiology

KW - Genetics of gene expression

KW - Statistical analysis of microarrays

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DO - 10.1007/s12561-009-9015-0

M3 - Review article

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VL - 1

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EP - 180

JO - Statistics in Biosciences

JF - Statistics in Biosciences

IS - 2

ER -

Processing and analyzing Affymetrix SNP chips with Bioconductor

Abstract

Keywords

ASJC Scopus subject areas

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