Nucleic Acids Research, 2001, Vol. 29, No. 12 2549-2557
© 2001 Oxford University Press
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.
* To whom correspondence should be addressed at: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA. Tel: +1 617 432 4912; Fax: +1 617 739 1781; Email: wwong{at}hsph.harvard.edu Correspondence may also be addressed to James C. Liao. Tel: +1 310 825 1656; Fax: +1 310 206 4107; Email: liaoj{at}ucla.edu The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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N. M. Luscombe, T. E. Royce, P. Bertone, N. Echols, C. E. Horak, J. T. Chang, M. Snyder, and M. Gerstein ExpressYourself: a modular platform for processing and visualizing microarray data Nucleic Acids Res., July 1, 2003; 31(13): 3477 - 3482. [Abstract] [Full Text] [PDF]
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 C Napoli, L O Lerman, V Sica, A Lerman, G Tajana, and F de Nigris Microarray analysis: a novel research tool for cardiovascular scientists and physicians Heart, June 1, 2003; 89(6): 597 - 604. [Abstract] [Full Text] [PDF]
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H. Yang, H. Haddad, C. Tomas, K. Alsaker, and E. T. Papoutsakis A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis PNAS, February 4, 2003; 100(3): 1122 - 1127. [Abstract] [Full Text] [PDF]
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G. Taroncher-Oldenburg, E. M. Griner, C. A. Francis, and B. B. Ward Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment Appl. Envir. Microbiol., February 1, 2003; 69(2): 1159 - 1171. [Abstract] [Full Text] [PDF]
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A. L. Drobyshev, C. Machka, M. Horsch, M. Seltmann, V. Liebscher, M. Hrabe de Angelis, and J. Beckers Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies Nucleic Acids Res., January 15, 2003; 31(2): e1 - e1. [Abstract] [Full Text] [PDF]
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 R. M. Braziel, M. A. Shipp, A. L. Feldman, V. Espina, M. Winters, E. S. Jaffe, E. F. Petricoin III, and L. A. Liotta Molecular Diagnostics Hematology, January 1, 2003; 2003(1): 279 - 293. [Abstract] [Full Text] [PDF]
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E. Sterrenburg, R. Turk, J. M. Boer, G. B. van Ommen, and J. T. den Dunnen A common reference for cDNA microarray hybridizations Nucleic Acids Res., November 1, 2002; 30(21): e116 - e116. [Abstract] [Full Text] [PDF]
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A. Dash, I. P. Maine, S. Varambally, R. Shen, A. M. Chinnaiyan, and M. A. Rubin Changes in Differential Gene Expression because of Warm Ischemia Time of Radical Prostatectomy Specimens Am. J. Pathol., November 1, 2002; 161(5): 1743 - 1748. [Abstract] [Full Text] [PDF]
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C. Virtanen, Y. Ishikawa, D. Honjoh, M. Kimura, M. Shimane, T. Miyoshi, H. Nomura, and M. H. Jones Integrated classification of lung tumors and cell lines by expression profiling PNAS, September 17, 2002; 99(19): 12357 - 12362. [Abstract] [Full Text] [PDF]
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T.-K. Jenssen, M. Langaas, W. P. Kuo, B. Smith-Sorensen, O. Myklebost, and E. Hovig Analysis of repeatability in spotted cDNA microarrays Nucleic Acids Res., July 15, 2002; 30(14): 3235 - 3244. [Abstract] [Full Text] [PDF]
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J.-J. Hwang, P. D. Allen, G. C. Tseng, C.-W. Lam, L. Fananapazir, V. J. Dzau, and C.-C. Liew Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure Physiol Genomics, July 12, 2002; 10(1): 31 - 44. [Abstract] [Full Text] [PDF]
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T. C. Kroll and S. Wolfl Ranking: a closer look on globalisation methods for normalisation of gene expression arrays Nucleic Acids Res., June 1, 2002; 30(11): e50 - e50. [Abstract] [Full Text] [PDF]
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M.-K. Oh, L. Rohlin, K. C. Kao, and J. C. Liao Global Expression Profiling of Acetate-grown Escherichia coli J. Biol. Chem., April 5, 2002; 277(15): 13175 - 13183. [Abstract] [Full Text] [PDF]
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R. Ramakrishnan, D. Dorris, A. Lublinsky, A. Nguyen, M. Domanus, A. Prokhorova, L. Gieser, E. Touma, R. Lockner, M. Tata, et al. An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications Nucleic Acids Res., April 1, 2002; 30(7): e30 - e30. [Abstract] [Full Text] [PDF]
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Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res., February 15, 2002; 30(4): e15 - e15. [Abstract] [Full Text] [PDF]
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S. L. Karsten, V. M. D. Van Deerlin, C. Sabatti, L. H. Gill, and D. H. Geschwind An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis Nucleic Acids Res., January 15, 2002; 30(2): e4 - e4. [Abstract] [Full Text] [PDF]
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