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Proceedings Paper

Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology
Author(s): David M. Haaland; Jerilyn A. Timlin; Michael B. Sinclair; Mark H. Van Benthem; M. Juanita Martinez; Anthony D. Aragon; Margaret Werner-Washburne
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Paper Abstract

Multivariate curve resolution (MCR) using constrained alternating least squares algorithms represents a powerful analysis capability for a quantitative analysis of hyperspectral image data. We will demonstrate the application of MCR using data from a new hyperspectral fluorescence imaging microarray scanner for monitoring gene expression in cells from thousands of genes on the array. The new scanner collects the entire fluorescence spectrum from each pixel of the scanned microarray. Application of MCR with nonnegativity and equality constraints reveals several sources of undesired fluorescence that emit in the same wavelength range as the reporter fluorphores. MCR analysis of the hyperspectral images confirms that one of the sources of fluorescence is due to contaminant fluorescence under the printed DNA spots that is spot localized. Thus, traditional background subtraction methods used with data collected from the current commercial microarray scanners will lead to errors in determining the relative expression of low-expressed genes. With the new scanner and MCR analysis, we generate relative concentration maps of the background, impurity, and fluroescent labels over the entire image. Since the concentration maps of the fluorescent labels are relativly uaffected by the presence of background and impurity emissions, the accuracy and useful dynamic range of the gene expression data are both greatly improved over those obtained by commercial microarray scanners.

Paper Details

Date Published: 2 July 2003
PDF: 12 pages
Proc. SPIE 4959, Spectral Imaging: Instrumentation, Applications, and Analysis II, (2 July 2003); doi: 10.1117/12.477945
Show Author Affiliations
David M. Haaland, Sandia National Labs. (United States)
Jerilyn A. Timlin, Sandia National Labs. (United States)
Michael B. Sinclair, Sandia National Labs. (United States)
Mark H. Van Benthem, Sandia National Labs. (United States)
M. Juanita Martinez, Univ. of New Mexico (United States)
Anthony D. Aragon, Univ. of New Mexico (United States)
Margaret Werner-Washburne, Univ. of New Mexico (United States)

Published in SPIE Proceedings Vol. 4959:
Spectral Imaging: Instrumentation, Applications, and Analysis II
Richard M. Levenson; Gregory H. Bearman; Anita Mahadevan-Jansen, Editor(s)

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