Affy - Analysis of Affymetrix GeneChip data at the probe level

Laurent Gautier; Leslie Cope; Benjamin M. Bolstad; Rafael A. Irizarry

doi:10.1093/bioinformatics/btg405

Affy - Analysis of Affymetrix GeneChip data at the probe level

Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry

School of Medicine

Research output: Contribution to journal › Article › peer-review

3303 Scopus citations

Abstract

Motivation: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. Results: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we presentthe main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.

Original language	English (US)
Pages (from-to)	307-315
Number of pages	9
Journal	Bioinformatics
Volume	20
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btg405
State	Published - Feb 12 2004

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btg405

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title = "Affy - Analysis of Affymetrix GeneChip data at the probe level",

abstract = "Motivation: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. Results: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we presentthe main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.",

author = "Laurent Gautier and Leslie Cope and Bolstad, {Benjamin M.} and Irizarry, {Rafael A.}",

note = "Funding Information: The authors would like to thank Robert Gentleman for his invaluable help through comments and suggestions. Special thanks is due as well to three anonymous reviewers who{\textquoteright}s recommendations did much to improve the paper. The work of L.G. is funded by the Danish Biotechnology Instrument Center. He would also like to acknowledge the microarrays, group at CBS, among particularly Steen Knudsen (lead) and Thomas Jensen (technical expertise on the experimental side), the Bioinformatics department of the Yang-Ming National University of Taiwan and the Dana-Farber Cancer Research Center, which computing facilities were used. The work of R.A.I. and L.M.C. is in-part supported by the Hopkins PGA (www.hopkins-genomics.org) Administrative/Bioinformatics Component (P01 HL 66583).",

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AU - Irizarry, Rafael A.

N1 - Funding Information: The authors would like to thank Robert Gentleman for his invaluable help through comments and suggestions. Special thanks is due as well to three anonymous reviewers who’s recommendations did much to improve the paper. The work of L.G. is funded by the Danish Biotechnology Instrument Center. He would also like to acknowledge the microarrays, group at CBS, among particularly Steen Knudsen (lead) and Thomas Jensen (technical expertise on the experimental side), the Bioinformatics department of the Yang-Ming National University of Taiwan and the Dana-Farber Cancer Research Center, which computing facilities were used. The work of R.A.I. and L.M.C. is in-part supported by the Hopkins PGA (www.hopkins-genomics.org) Administrative/Bioinformatics Component (P01 HL 66583).

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Affy - Analysis of Affymetrix GeneChip data at the probe level

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