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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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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S. Glyn-Jones, S. Song, M. A. Black, A. R. J. Phillips, S. Y. Choong, and G. J. S. Cooper Transcriptomic analysis of the cardiac left ventricle in a rodent model of diabetic cardiomyopathy: molecular snapshot of a severe myocardial disease Physiol Genomics, February 12, 2007; 28(3): 284 - 293. [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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D. S. Yuan and R. A. Irizarry High-resolution spatial normalization for microarrays containing embedded technical replicates Bioinformatics, December 15, 2006; 22(24): 3054 - 3060. [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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S. Yoon, Y. Yang, J. Choi, and J. Seong Large scale data mining approach for gene-specific standardization of microarray gene expression data Bioinformatics, December 1, 2006; 22(23): 2898 - 2904. [Abstract] [Full Text] [PDF]
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P. C. LaRosa, J. Miner, Y. Xia, Y. Zhou, S. Kachman, and M. E. Fromm Trans-10, cis-12 conjugated linoleic acid causes inflammation and delipidation of white adipose tissue in mice: a microarray and histological analysis Physiol Genomics, November 21, 2006; 27(3): 282 - 294. [Abstract] [Full Text] [PDF]
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J. E. Zimmerman, W. Rizzo, K. R. Shockley, D. M. Raizen, N. Naidoo, M. Mackiewicz, G. A. Churchill, and A. I. Pack Multiple mechanisms limit the duration of wakefulness in Drosophila brain Physiol Genomics, November 21, 2006; 27(3): 337 - 350. [Abstract] [Full Text] [PDF]
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J. Vendelin, S. Bruce, P. Holopainen, V. Pulkkinen, P. Rytila, A. Pirskanen, M. Rehn, T. Laitinen, L. A. Laitinen, T. Haahtela, et al. Downstream target genes of the neuropeptide S-NPSR1 pathway Hum. Mol. Genet., October 1, 2006; 15(19): 2923 - 2935. [Abstract] [Full Text] [PDF]
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X. Cui, J. Affourtit, K. R. Shockley, Y. Woo, and G. A. Churchill Inheritance Patterns of Transcript Levels in F1 Hybrid Mice Genetics, October 1, 2006; 174(2): 627 - 637. [Abstract] [Full Text] [PDF]
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D. Abdueva, D. Skvortsov, and S. Tavare Non-linear analysis of GeneChip arrays Nucleic Acids Res., September 10, 2006; 34(15): e105 - e105. [Abstract] [Full Text] [PDF]
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M. A. Hannah, D. Wiese, S. Freund, O. Fiehn, A. G. Heyer, and D. K. Hincha Natural Genetic Variation of Freezing Tolerance in Arabidopsis Plant Physiology, September 1, 2006; 142(1): 98 - 112. [Abstract] [Full Text] [PDF]
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