Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.
affy—analysis of Affymetrix GeneChip data at the probe level
1 Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Building 208, 2800 Lyngby, Denmark, 2 Department of Mathematical Sciences, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA, 3 Group in Biostatistics, University of California, Berkeley, CA 94720, USA and 4 Department of Biostatistics, Johns Hopkins University, 615 N. Wolfe St E3035, Baltimore, MD 21218, USA
Received on April 21, 2003
; revised on July 4, 2003
; accepted on July 11, 2003
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 present the 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.
Contact: laurent{at}cbs.dtu.dk
* To whom correspondence should be addressed.
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M. Mackiewicz, K. R. Shockley, M. A. Romer, R. J. Galante, J. E. Zimmerman, N. Naidoo, D. A. Baldwin, S. T. Jensen, G. A. Churchill, and A. I. Pack Macromolecule biosynthesis: a key function of sleep Physiol Genomics, November 14, 2007; 31(3): 441 - 457. [Abstract] [Full Text] [PDF]
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R. Stewart, W. Wei, A. Challa, R. J. Armitage, J. R. Arrand, M. Rowe, L. S. Young, A. Eliopoulos, and J. Gordon CD154 Tone Sets the Signaling Pathways and Transcriptome Generated in Model CD40-Pluricompetent L3055 Burkitt's Lymphoma Cells J. Immunol., September 1, 2007; 179(5): 2705 - 2712. [Abstract] [Full Text] [PDF]
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M. J. Dunning, M. L. Smith, M. E. Ritchie, and S. Tavare beadarray: R classes and methods for Illumina bead-based data Bioinformatics, August 15, 2007; 23(16): 2183 - 2184. [Abstract] [Full Text] [PDF]
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A. Kuhn, D. R. Goldstein, A. Hodges, A. D. Strand, T. Sengstag, C. Kooperberg, K. Becanovic, M. A. Pouladi, K. Sathasivam, J.-H. J. Cha, et al. Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage Hum. Mol. Genet., August 1, 2007; 16(15): 1845 - 1861. [Abstract] [Full Text] [PDF]
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M. Touma, V. Antonini, M. Kumar, S. L. Osborn, A. M. Bobenchik, D. B. Keskin, J. E. Connolly, M. J. Grusby, E. L. Reinherz, and L. K. Clayton Functional Role for I{kappa}BNS in T Cell Cytokine Regulation As Revealed by Targeted Gene Disruption J. Immunol., August 1, 2007; 179(3): 1681 - 1692. [Abstract] [Full Text] [PDF]
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R. M. Graze, O. Barmina, D. Tufts, E. Naderi, K. L. Harmon, M. Persianinova, and S. V. Nuzhdin New Candidate Genes for Sex-Comb Divergence Between Drosophila mauritiana and Drosophila simulans Genetics, August 1, 2007; 176(4): 2561 - 2576. [Abstract] [Full Text] [PDF]
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W. K. Lim, K. Wang, C. Lefebvre, and A. Califano Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks Bioinformatics, July 1, 2007; 23(13): i282 - i288. [Abstract] [Full Text] [PDF]
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S. A. Eschrich and A. M. Hoerter Libaffy: software for processing Affymetrix(R) GeneChip(R) data Bioinformatics, June 15, 2007; 23(12): 1562 - 1564. [Abstract] [Full Text] [PDF]
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G. M. Bruun, R. Wernersson, A. S. Juncker, H. Willenbrock, and H. B. Nielsen Improving comparability between microarray probe signals by thermodynamic intensity correction Nucleic Acids Res., April 1, 2007; 35(7): e48 - e48. [Abstract] [Full Text] [PDF]
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T. M. Dame, B. L. Orenzoff, L. E. Palmer, and M. B. Furie IFN-{gamma} Alters the Response of Borrelia burgdorferi-Activated Endothelium to Favor Chronic Inflammation J. Immunol., January 15, 2007; 178(2): 1172 - 1179. [Abstract] [Full Text] [PDF]
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H. Crandall, D. M. Dunn, Y. Ma, R. M. Wooten, J. F. Zachary, J. H. Weis, R. B. Weiss, and J. J. Weis Gene Expression Profiling Reveals Unique Pathways Associated with Differential Severity of Lyme Arthritis J. Immunol., December 1, 2006; 177(11): 7930 - 7942. [Abstract] [Full Text] [PDF]
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