Differentiation detection in microarray normalization

Methods in Microarray Normalization

Volumn , Issue , 2008, Pages 19-39

  Li, Lei M ^a   Cheng, Chao ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77952246516     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (28)

1. Affymetrix. Affymetrix microarray suite user guide, 5th ed. Santa Clara, CA: Affymetrix 2001.
2. A. Bhattacharjee, W. G. Richards, J. Staunton, C. Li, S. Monti, P. Vasa, C. Ladd, et al. Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. PNAS, 98:13790–13795, 2001.
3. B. M. Bolstad, R. A. Irizarry, M. Astrand, and T. P. Speed. A comparison of normalization methods for high-density oligonucleotide array data based on bias and variance. Bioinformatics, 19:185–193, 2003.
4. M. Caceres, J. Lachuer, A. M. Zapala, C. J. Redmond, L. Kudo, H. D. Geschwind, J. D. Lockhart, et al. Elevated gene expression levels distinguish human from nonhuman primate brains. Proceedings of the National Academy of Science, USA, 100:13030–13035, 2003.
5. C. Cheng. Symmetric and trimmed solutions of simple linear regression. Master’s thesis, University of Southern California, 2006.
6. W. S. Cleveland. Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association, 74:829–836, 1979.
7. B. P. Durbin, J. S. Hardin, D. M. Hawkins, and D. M. Rocke. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics, 18:S105–S110, 2002.
8. W. Enard, P. Khaitovich, J. Klose, S. Zöllner, F. Heissig, P. Giavalisco, S. K. Nieselt, et al. Intra-and interspecific variation in primate gene expression patterns. Science, 296:340–343, 2002.
9. J. Gu and X. Gu. Induced gene expression in human brain after the split from chimpanzee. Trends in Genetics, 19:63–65, 2003.
10. W. Huber, V. A. Heydebreck, H. Sültmann, A. Poustka, and M. Vingron. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18:S96–S104, 2002.
11. R. A. Irizarry, B. Hobbs, F. Collin, Y. D. Beazer-Barclay, K. J. Antonellis, U. Scherf, and T. P. Speed. Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. Biostatistics, 4:249–264, 2003.
12. T. Kepler, L. Crosby, and K. Morgan. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biology, 3:1–12, 2002.
13. C. Li and W. H. Wong. Model-based analysis of oligonucleotide arrays: Model validation, design issues, and standard error applications. Genome Biology, 2:1–11, 2001.
14. L. M. Li. Blind inversion needs distribution (BIND): The general notion and case studies. In D. Goldstein, ed., Science and statistics: A Festschrift for Terry Speed, volume 40, pp. 273–293. Institute of Mathematical Statistics, 2003.
15. L. M. Li. An algorithm for computing exact least trimmed squares estimate of simple linear regression with constraints. Computational Statistics and Data Analysis, 48:717–734, 2004.
16. D. J. Lockhart, H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, et al. DNA expression monitoring by hybridization of high density oligonucleotide arrays. Nature Biotechnology, 14:1675–1680, 1996.
17. P. J. Rousseeuw and A. M. Leroy. Robust regression and outlier detection. New York: Wiley, 1987.
18. E. E. Schadt, C. Li, C. Su, and W. H. Wong. Analyzing high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry, 80:192–202, 2000.
19. E. E. Schadt, C. Li, B. Ellis, and W. H. Wong. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry, supplement 37:120–125, 2001.
20. L. Shi, W. Tong, Z. Su, T. Han, J. Han, R. K. Puri, H. Fang, et al. Microarray scanner calibration curves: Characteristics and implications. BMC Bioinformatics, 6(Suppl 2), 2:S11, 2005.
21. I. A. Sidorov, D. A. Hosack, D. Gee, J. Yang, M. C. Cam, R. A. Lempicki, and D. S. Dimitrov. Oligonucleotide microarray data distribution and normalization. Information Sciences, 146:67–73, 2002.
22. G. C. Tseng, M. K. Oh, L. Rohlin, J. C. Liao, and W. H. Wong. Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations, and assessment of gene effects. Nucleic Acids Research, 29:2549–2557, 2001.
23. J. van de Peppel, P. Kemmeren, H. van Bakel, M. Radonjic, D. van Leenen, and F. C. P. Holstege. Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Reports, 4:387–393, 2003.
24. C. Workman, J. L. Jensen, H. Jarmer, R. Berka, L. Gautier, B. H. Nielsen, H. Saxild, et al. A new nonlinear normalization method for reducing variability in DNA microarray experiments. Genome Biology, 3:1–16, 2002.
25. Z. Wu and R. A. Irizarry. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. RECOMB, 98–106, 2004.
26. 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 Research, 30:e15, 2002.
27. Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed. Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty, eds., Microarrays: Optical technologies and informatics, volume 4266. SPIE, 2001.
28. A. Zien, T. Aigner, R. Zimmer, and T. Lengauer. Centralization: A new method for the normalization of gene expression data. Bioinformatics, 17:323–331, 2001.