The DOI matches its Crossref record; 17 of the 17 references it cites were found in a registry or an index.
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
Open accessAbstract
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.
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Modern Applied Statistics with S
Venables, W. N., & Ripley, B. D. (2002) · Statistics and Computing · doi:10.1007/978-0-387-21706-2 · Cited by 24,305
Markov Chain Monte Carlo in Practice
(1995) · Chapman & Hall/CRC eBooks · doi:10.1201/b14835 · Cited by 7,757
The Complete Genome Sequence of Escherichia coli K-12
Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,452
Miller, J. H. (1992) · Medical Entomology and Zoology · Cited by 2,488
Exploring the new world of the genome with DNA microarrays
Brown, P. O., & Botstein, D. (1999) · Nature Genetics · doi:10.1038/4462 · Cited by 2,414
Dudoit, S., Yang, J. Y. H., Callow, M. J., & Speed, T. P. (2002) · Cited by 1,392
Analysis of Variance for Gene Expression Microarray Data
Kerr, M. K., Martin, M., & Churchill, G. A. (2000) · Journal of Computational Biology · doi:10.1089/10665270050514954 · Cited by 1,310
[12] DNA arrays for analysis of gene expression
Eisen, M. B., & Brown, P. O. (1999) · Methods in Enzymology · doi:10.1016/s0076-6879(99)03014-1 · Cited by 1,032
Lee, M.-L. T., Kuo, F. C., Whitmore, G. A., & Sklar, J. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.18.9834 · Cited by 861
Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blattner, F. R., & Tsui, K. W. (2001) · Journal of Computational Biology · doi:10.1089/106652701300099074 · Cited by 739
Cited by
Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., & Speleman, F. (2002) · Genome Biology · doi:10.1186/gb-2002-3-7-research0034 · Cited by 20,038
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658
Kolpin, D. W., Furlong, E. T., Meyer, M. T., Thurman, E. M., Zaugg, S. D., Barber, L. B., & Buxton, H. T. (2002) · Environmental Science & Technology · doi:10.1021/es011055j · Cited by 7,953
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
Leek, J. T., & Storey, J. D. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030161 · Cited by 1,930
Microarray data normalization and transformation
Quackenbush, J. (2002) · Nature Genetics · doi:10.1038/ng1032 · Cited by 1,975
Metadata
- Authors
- Tseng, G. C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-06-15
- Volume
- 29
- Issue
- 12
- Pages
- 2549-2557
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2099114361
- Cited by
- 572
- References
- 17
- FWCI
- 20.63
- Type
- journal article
- Language
- en
- Open access
- green
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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