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Proceedings Paper

Estimation of the confidence limits of oligonucleotide-array-based measurements of differential expression
Author(s): Glenda Delenstarr; Herb Cattell; Chao Chen; Andreas N. Dorsel; Robert H. Kincaid; Khanh Nguyen; Nicholas M. Sampas; Shad Schidel; Karen W. Shannon; Andrea Tu; Paul K. Wolber
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Paper Abstract

Microarrays can be used to simultaneously measure the differential expression states of many mRNA's in two samples. Such measurements are limited by systematic and random errors. Systematic errors include labeling bias, imperfect feature morphologies, mismatched sample concentrations, and cross-hybridization. Random errors arise from chemical and scanning noise, particularly for low signals. We have used a combination of fluor-exchanged two- color labeling and improved normalization methods to minimize systematic errors from labeling bias, imperfect features, and mismatched sample concentrations. On-array specificity control proves and experimentally proven probe design algorithms were used to correct for cross- hybridization. Random errors were reduced via automated non-uniform feature flagging and an advanced scanner design. We have scored feature significance, using established statistical tests. We have then estimated the intrinsic random measurement error as a function of average probe signal via sample self-comparison experiments (human K-562 cell mRNA). Finally, we have combined all of these tools in the analysis of differential expression measurements between K-562 cells and HeLa cells. The results establish the importance of the elimination of systematic errors and the objective assessment of the effects of random errors in producing reliable estimates of differential expression.

Paper Details

Date Published: 4 June 2001
PDF: 12 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427980
Show Author Affiliations
Glenda Delenstarr, Agilent Technologies (United States)
Herb Cattell, Agilent Technologies (United States)
Chao Chen, Agilent Technologies (United States)
Andreas N. Dorsel, Agilent Technologies (United States)
Robert H. Kincaid, Agilent Technologies (United States)
Khanh Nguyen, Agilent Technologies (United States)
Nicholas M. Sampas, Agilent Technologies (United States)
Shad Schidel, Agilent Technologies (United States)
Karen W. Shannon, Agilent Technologies (United States)
Andrea Tu, Agilent Technologies (United States)
Paul K. Wolber, Agilent Technologies (United States)

Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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