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Proceedings Paper

Groundtruth approach to accurate quantitation of fluorescence microarrays
Author(s): Laura Mascio Kegelmeyer; Lisa Tomascik-Cheeseman; Melinda S. Burnett; Paul van Hummelen; Andrew J. Wyrobek
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Paper Abstract

To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results substantially closer to the known groundtruth for these samples.

Paper Details

Date Published: 4 June 2001
PDF: 11 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427998
Show Author Affiliations
Laura Mascio Kegelmeyer, Lawrence Livermore National Lab. (United States)
Lisa Tomascik-Cheeseman, Lawrence Livermore National Lab. (United States)
Melinda S. Burnett, Lawrence Livermore National Lab. (United States)
Paul van Hummelen, Lawrence Livermore National Lab. (United States)
Andrew J. Wyrobek, Lawrence Livermore National Lab. (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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