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Proceedings Paper

Statistical issues in signal extraction from microarrays
Author(s): Tracy Bergemann; Filemon Quiaoit; Jeffrey J. Delrow; Lue Ping Zhao
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Paper Abstract

Microarray technologies are increasingly used in biomedical research to study genome-wide expression profiles in the post genomic era. Their popularity is largely due to their high throughput and economical affordability. For example, microarrays have been applied to studies of cell cycle, regulatory circuitry, cancer cell lines, tumor tissues, and drug discoveries. One obstacle facing the continued success of applying microarray technologies, however, is the random variaton present on microarrays: within signal spots, between spots and among chips. In addition, signals extracted by available software packages seem to vary significantly. Despite a variety of software packages, it appears that there are two major approaches to signal extraction. One approach is to focus on the identification of signal regions and hence estimation of signal levels above background levels. The other approach is to use the distribution of intensity values as a way of identifying relevant signals. Building upon both approaches, the objective of our work is to develop a method that is statistically rigorous and also efficient and robust. Statistical issues to be considered here include: (1) how to refine grid alignment so that the overall variation is minimized, (2) how to estimate the signal levels relative to the local background levels as well as the variance of this estimate, and (3) how to integrate red and green channel signals so that the ratio of interest is stable, simultaneously relaxing distributional assumptions.

Paper Details

Date Published: 4 June 2001
PDF: 11 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427997
Show Author Affiliations
Tracy Bergemann, Univ. of Washington School of Public Health (United States)
Filemon Quiaoit, Fred Hutchinson Cancer Research Ctr. (United States)
Jeffrey J. Delrow, Fred Hutchinson Cancer Research Ctr. (United States)
Lue Ping Zhao, Fred Hutchinson Cancer Research Ctr. (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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