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Proceedings Paper

Rank-based algorithms for anlaysis of microarrays
Author(s): Wei-min Liu; Rui Mei; Daniel M. Bartell; Xiaojun Di; Teresa A. Webster; Tom Ryder
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Paper Abstract

Analysis of microarray data often involves extracting information from raw intensities of spots of cells and making certain calls. Rank-based algorithms are powerful tools to provide probability values of hypothesis tests, especially when the distribution of the intensities is unknown. For our current gene expression arrays, a gene is detected by a set of probe pairs consisting of perfect match and mismatch cells. The one-sided upper-tail Wilcoxon's signed rank test is used in our algorithms for absolute calls (whether a gene is detected or not), as well as comparative calls (whether a gene is increasing or decreasing or no significant change in a sample compared with another sample). We also test the possibility to use only perfect match cells to make calls. This paper focuses on absolute calls. We have developed error analysis methods and software tools that allow us to compare the accuracy of the calls in the presence or absence of mismatch cells at different target concentrations. The usage of nonparametric rank-based tests is not limited to absolute and comparative calls of gene expression chips. They can also be applied to other oligonucleotide microarrays for genotyping and mutation detection, as well as spotted arrays.

Paper Details

Date Published: 4 June 2001
PDF: 12 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.428000
Show Author Affiliations
Wei-min Liu, Affymetrix, Inc. (United States)
Rui Mei, Affymetrix, Inc. (United States)
Daniel M. Bartell, Affymetrix, Inc. (United States)
Xiaojun Di, Affymetrix, Inc. (United States)
Teresa A. Webster, Affymetrix, Inc. (United States)
Tom Ryder, Affymetrix, Inc. (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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