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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C. R. Antonescu, A. Yoshida, T. Guo, N.-E. Chang, L. Zhang, N. P. Agaram, L.-X. Qin, M. F. Brennan, S. Singer, and R. G. Maki KDR Activating Mutations in Human Angiosarcomas Are Sensitive to Specific Kinase Inhibitors Cancer Res., September 15, 2009; 69(18): 7175 - 7179. [Abstract] [Full Text] [PDF]
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J. T. Judy and H. Ji TileProbe: modeling tiling array probe effects using publicly available data Bioinformatics, September 15, 2009; 25(18): 2369 - 2375. [Abstract] [Full Text] [PDF]
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 D. Del Duca, G. Wong, P. Trieu, D. Rodaros, A. Kouremenos, A. Tadevosyan, G. Vaniotis, L. R. Villeneuve, C. I. Tchervenkov, S. Nattel, et al. Association of neonatal hypoxia with lasting changes in left ventricular gene expression: An animal model J. Thorac. Cardiovasc. Surg., September 1, 2009; 138(3): 538 - 546. [Abstract] [Full Text] [PDF]
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 M. MORAL, C. SEGRELLES, A. B. MARTINEZ-CRUZ, C. LORZ, M. SANTOS, R. GARCIA-ESCUDERO, J. LU, A. BUITRAGO, C. COSTA, C. SAIZ, et al. Transgenic Mice Expressing Constitutively Active Akt in Oral Epithelium Validate KLFA as a Potential Biomarker of Head and Neck Squamous Cell Carcinoma In Vivo, September 1, 2009; 23(5): 653 - 660. [Abstract] [Full Text] [PDF]
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D. Gaidatzis, K. Jacobeit, E. J. Oakeley, and M. B. Stadler Overestimation of alternative splicing caused by variable probe characteristics in exon arrays Nucleic Acids Res., September 1, 2009; 37(16): e107 - e107. [Abstract] [Full Text] [PDF]
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 G. Frank, E. Pressman, R. Ophir, L. Althan, R. Shaked, M. Freedman, S. Shen, and N. Firon Transcriptional profiling of maturing tomato (Solanum lycopersicum L.) microspores reveals the involvement of heat shock proteins, ROS scavengers, hormones, and sugars in the heat stress response J. Exp. Bot., September 1, 2009; 60(13): 3891 - 3908. [Abstract] [Full Text] [PDF]
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F. Martinelli, S. L. Uratsu, R. L. Reagan, Y. Chen, D. Tricoli, O. Fiehn, D. M. Rocke, C. S. Gasser, and A. M. Dandekar Gene regulation in parthenocarpic tomato fruit J. Exp. Bot., September 1, 2009; 60(13): 3873 - 3890. [Abstract] [Full Text] [PDF]
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B. J. White, C. Cheng, D. Sangare, N. F. Lobo, F. H. Collins, and N. J. Besansky The Population Genomics of Trans-Specific Inversion Polymorphisms in Anopheles gambiae Genetics, September 1, 2009; 183(1): 275 - 288. [Abstract] [Full Text] [PDF]
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C.-W. Lee, M. Efetova, J. C Engelmann, R. Kramell, C. Wasternack, J. Ludwig-Muller, R. Hedrich, and R. Deeken Agrobacterium tumefaciens Promotes Tumor Induction by Modulating Pathogen Defense in Arabidopsis thaliana PLANT CELL, September 1, 2009; 21(9): 2948 - 2962. [Abstract] [Full Text] [PDF]
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 G. Miller, K. Schlauch, R. Tam, D. Cortes, M. A. Torres, V. Shulaev, J. L. Dangl, and R. Mittler The Plant NADPH Oxidase RBOHD Mediates Rapid Systemic Signaling in Response to Diverse Stimuli Sci. Signal., August 18, 2009; 2(84): ra45 - ra45. [Abstract] [Full Text] [PDF]
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A. Patino-Garcia, M. Zalacain, C. Folio, C. Zandueta, L. Sierrasesumaga, M. San Julian, G. Toledo, J. De Las Rivas, and F. Lecanda Profiling of Chemonaive Osteosarcoma and Paired-Normal Cells Identifies EBF2 as a Mediator of Osteoprotegerin Inhibition to Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand-Induced Apoptosis Clin. Cancer Res., August 15, 2009; 15(16): 5082 - 5091. [Abstract] [Full Text] [PDF]
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P. Camateros, C. Kanagaratham, J. Henri, R. Sladek, T. J. Hudson, and D. Radzioch Modulation of the allergic asthma transcriptome following resiquimod treatment Physiol Genomics, August 7, 2009; 38(3): 303 - 318. [Abstract] [Full Text] [PDF]
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D. J. Pappas, G. Coppola, P. A. Gabatto, F. Gao, D. H. Geschwind, J. R. Oksenberg, and S. E. Baranzini Longitudinal system-based analysis of transcriptional responses to type I interferons Physiol Genomics, August 7, 2009; 38(3): 362 - 371. [Abstract] [Full Text] [PDF]
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 K. S. Collison, Z. Maqbool, S. M. Saleh, A. Inglis, N. J. Makhoul, R. Bakheet, M. Al-Johi, R. Al-Rabiah, M. Z. Zaidi, and F. A. Al-Mohanna Effect of dietary monosodium glutamate on trans fat-induced nonalcoholic fatty liver disease J. Lipid Res., August 1, 2009; 50(8): 1521 - 1537. [Abstract] [Full Text] [PDF]
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Y. Chen, G. Lin, J. S. Huo, D. Barney, Z. Wang, T. Livshiz, D. J. States, Z. S. Qin, and J. Schwartz Computational and Functional Analysis of Growth Hormone (GH)-Regulated Genes Identifies the Transcriptional Repressor B-Cell Lymphoma 6 (Bc16) as a Participant in GH-Regulated Transcription Endocrinology, August 1, 2009; 150(8): 3645 - 3654. [Abstract] [Full Text] [PDF]
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 A. B. MARTINEZ-CRUZ, M. SANTOS, R. GARCIA-ESCUDERO, M. MORAL, C. SEGRELLES, C. LORZ, C. SAIZ, A. BUITRAGO-PEREZ, C. COSTA, and J. M. PARAMIO Spontaneous Tumor Formation in Trp53-deficient Epidermis Mediated by Chromosomal Instability and Inflammation Anticancer Res, August 1, 2009; 29(8): 3035 - 3042. [Abstract] [Full Text] [PDF]
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P. Guo, M. Baum, S. Grando, S. Ceccarelli, G. Bai, R. Li, M. von Korff, R. K. Varshney, A. Graner, and J. Valkoun Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage J. Exp. Bot., August 1, 2009; 60(12): 3531 - 3544. [Abstract] [Full Text] [PDF]
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L. M. Matzkin and T. A. Markow Transcriptional Regulation of Metabolism Associated With the Increased Desiccation Resistance of the Cactophilic Drosophila mojavensis Genetics, August 1, 2009; 182(4): 1279 - 1288. [Abstract] [Full Text] [PDF]
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P. Pesaresi, A. Hertle, M. Pribil, T. Kleine, R. Wagner, H. Strissel, A. Ihnatowicz, V. Bonardi, M. Scharfenberg, A. Schneider, et al. Arabidopsis STN7 Kinase Provides a Link between Short- and Long-Term Photosynthetic Acclimation PLANT CELL, August 1, 2009; 21(8): 2402 - 2423. [Abstract] [Full Text] [PDF]
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D. Volodarsky, N. Leviatan, A. Otcheretianski, and R. Fluhr HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome Plant Physiology, August 1, 2009; 150(4): 1796 - 1805. [Abstract] [Full Text] [PDF]
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N. Hu, C. Wang, D. Ng, R. Clifford, H. H. Yang, Z.-Z. Tang, Q.-H. Wang, X.-Y. Han, C. Giffen, A. M. Goldstein, et al. Genomic Characterization of Esophageal Squamous Cell Carcinoma from a High-Risk Population in China Cancer Res., July 15, 2009; 69(14): 5908 - 5917. [Abstract] [Full Text] [PDF]
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 Y. Maruyama, Y. Nakamichi, T. Itoh, B. Mikami, W. Hashimoto, and K. Murata Substrate Specificity of Streptococcal Unsaturated Glucuronyl Hydrolases for Sulfated Glycosaminoglycan J. Biol. Chem., July 3, 2009; 284(27): 18059 - 18069. [Abstract] [Full Text] [PDF]
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 S. G. Dorsey, C. C. Leitch, C. L. Renn, S. Lessans, B. A. Smith, X. M. Wang, and R. A. Dionne Genome-Wide Screen Identifies Drug-Induced Regulation of the Gene Giant Axonal Neuropathy (Gan) in a Mouse Model of Antiretroviral-Induced Painful Peripheral Neuropathy Biol Res Nurs, July 1, 2009; 11(1): 7 - 16. [Abstract] [PDF]
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