Biostatistics 4:249-264 (2003)
© 2003 Oxford University Press
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Department of Biostatistics, Johns Hopkins University, Baltimore MD 21205, USA rafa{at}jhu.edu
Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia
Gene Logic Inc., Berkeley, CA, USA
Gene Logic Inc., Gaithersburg, MD, USA
Gene Logic Inc., Gaithersburg, MD, USA
Gene Logic Inc., Gaithersburg, MD, USA
Division of Genetics and Bioinformatics, WEHI, Melbourne, Australia. Department of Statistics, University of California at Berkeley
*To whom correspondence should be addressed
In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip® system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of five MGU74A mouse GeneChip® arrays, part of the data from an extensive spike-in study conducted by Gene Logic and Wyeth's Genetics Institute involving 95 HG-U95A human GeneChip® arrays; and part of a dilution study conducted by Gene Logic involving 75 HG-U95A GeneChip® arrays. We display some familiar features of the perfect match and mismatch probe (PM and MM) values of these data, and examine the variance–mean relationship with probe-level data from probes believed to be defective, and so delivering noise only. We explain why we need to normalize the arrays to one another using probe level intensities. We then examine the behavior of the PM and MM using spike-in data and assess three commonly used summary measures: Affymetrix's (i) average difference (AvDiff) and (ii) MAS 5.0 signal, and (iii) the Li and Wong multiplicative model-based expression index (MBEI). The exploratory data analyses of the probe level data motivate a new summary measure that is a robust multi-array average (RMA) of background-adjusted, normalized, and log-transformed PM values. We evaluate the four expression summary measures using the dilution study data, assessing their behavior in terms of bias, variance and (for MBEI and RMA) model fit. Finally, we evaluate the algorithms in terms of their ability to detect known levels of differential expression using the spike-in data. We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities.
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E. Oh, H. Kang, S. Yamaguchi, J. Park, D. Lee, Y. Kamiya, and G. Choi Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis PLANT CELL, February 1, 2009; 21(2): 403 - 419. [Abstract] [Full Text] [PDF]
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R. D. Meng, C. C. Shelton, Y.-M. Li, L.-X. Qin, D. Notterman, P. B. Paty, and G. K. Schwartz {gamma}-Secretase Inhibitors Abrogate Oxaliplatin-Induced Activation of the Notch-1 Signaling Pathway in Colon Cancer Cells Resulting in Enhanced Chemosensitivity Cancer Res., January 15, 2009; 69(2): 573 - 582. [Abstract] [Full Text] [PDF]
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F. Huang, A. Greer, W. Hurlburt, X. Han, R. Hafezi, G. M. Wittenberg, K. Reeves, J. Chen, D. Robinson, A. Li, et al. The Mechanisms of Differential Sensitivity to an Insulin-like Growth Factor-1 Receptor Inhibitor (BMS-536924) and Rationale for Combining with EGFR/HER2 Inhibitors Cancer Res., January 1, 2009; 69(1): 161 - 170. [Abstract] [Full Text] [PDF]
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A. L. Tarca, S. Draghici, P. Khatri, S. S. Hassan, P. Mittal, J.-s. Kim, C. J. Kim, J. P. Kusanovic, and R. Romero A novel signaling pathway impact analysis Bioinformatics, January 1, 2009; 25(1): 75 - 82. [Abstract] [Full Text] [PDF]
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H. Shen, N. Powers, N. Saini, C. E.S. Comstock, A. Sharma, K. Weaver, M. P. Revelo, W. Gerald, E. Williams, W. J. Jessen, et al. The SWI/SNF ATPase Brm Is a Gatekeeper of Proliferative Control in Prostate Cancer Cancer Res., December 15, 2008; 68(24): 10154 - 10162. [Abstract] [Full Text] [PDF]
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K. Kapur, H. Jiang, Y. Xing, and W. H. Wong Cross-hybridization modeling on Affymetrix exon arrays Bioinformatics, December 15, 2008; 24(24): 2887 - 2893. [Abstract] [Full Text] [PDF]
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H. M. Kang, C. Ye, and E. Eskin Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots Genetics, December 1, 2008; 180(4): 1909 - 1925. [Abstract] [Full Text] [PDF]
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S. Malitsky, E. Blum, H. Less, I. Venger, M. Elbaz, S. Morin, Y. Eshed, and A. Aharoni The Transcript and Metabolite Networks Affected by the Two Clades of Arabidopsis Glucosinolate Biosynthesis Regulators Plant Physiology, December 1, 2008; 148(4): 2021 - 2049. [Abstract] [Full Text] [PDF]
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A. Rodriguez-Caballero, A. C. Garcia-Montero, P. Barcena, J. Almeida, F. Ruiz-Cabello, M. D. Tabernero, P. Garrido, S. Munoz-Criado, Y. Sandberg, A. W. Langerak, et al. Expanded cells in monoclonal TCR-{alpha}{beta}+/CD4+/NKa+/CD8-/+dim T-LGL lymphocytosis recognize hCMV antigens Blood, December 1, 2008; 112(12): 4609 - 4616. [Abstract] [Full Text] [PDF]
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Y.-C. L. Tung, M. Ma, S. Piper, A. Coll, S. O'Rahilly, and G. S. H. Yeo Novel Leptin-Regulated Genes Revealed by Transcriptional Profiling of the Hypothalamic Paraventricular Nucleus J. Neurosci., November 19, 2008; 28(47): 12419 - 12426. [Abstract] [Full Text] [PDF]
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R. E. Drew, K. J. Rodnick, M. Settles, J. Wacyk, E. Churchill, M. S. Powell, R. W. Hardy, G. K. Murdoch, R. A. Hill, and B. D. Robison Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio) Physiol Genomics, November 12, 2008; 35(3): 283 - 295. [Abstract] [Full Text] [PDF]
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A. N. Simms and H. L. T. Mobley PapX, a P Fimbrial Operon-Encoded Inhibitor of Motility in Uropathogenic Escherichia coli Infect. Immun., November 1, 2008; 76(11): 4833 - 4841. [Abstract] [Full Text] [PDF]
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L. Xi, A. Feber, V. Gupta, M. Wu, A. D. Bergemann, R. J. Landreneau, V. R. Litle, A. Pennathur, J. D. Luketich, and T. E. Godfrey Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer Nucleic Acids Res., November 1, 2008; 36(20): 6535 - 6547. [Abstract] [Full Text] [PDF]
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