Faculty Collaboration Database

A novel approach for high-quality microarray processing using third-dye array visualization technology. IEEE Trans Nanobioscience 2003 Dec;2(4):193-201

Date

09/21/2004

Pubmed ID

15376909

DOI

10.1109/tnb.2003.816233

Scopus ID

2-s2.0-2442672221 (requires institutional sign-in at Scopus site)   15 Citations

Abstract

Historically, microarray image processing has been technically challenging in obtaining quality gene expression data. After hybridization of Cy3- and Cy5-labeled samples, images are collected and processed to obtain gene expression ratio measurements for each of the elements on the array. The hybridization process often brings in contaminating noise, which can make correct identification of the signal difficult. In addition, spot intensity levels are highly variable due to the expression differences of different genes, and weak spots are often difficult to detect. These conditions are further complicated by inherent irregularities in spot position, shape, and size commonly found on high-density microarrays, making image processing an often labor-intensive task that is difficult to reliably automate. We previously reported a novel third-dye array visualization (TDAV) technology that allows prehybridization visualization and quality control of printed arrays. Here, we present a new microarray image processing approach utilizing TDAV. By incorporating the third-dye image, we show that overall quality of the microarray data is significantly improved, and automation of processing is feasible and reliable. Furthermore, we demonstrate use of the third-dye image to better quality control microarray image analysis. Both the principle and implementation of the approach are presented in detail, with experimental results.

Author List

Wang X, Jiang N, Feng X, Xie Y, Tonellato PJ, Ghosh S, Hessner MJ

Author

Martin J. Hessner PhD Professor in the Pediatrics department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Algorithms
DNA
Fluorescent Dyes
Gene Expression Profiling
Image Enhancement
Image Interpretation, Computer-Assisted
Microscopy, Fluorescence
Nanotechnology
Oligonucleotide Array Sequence Analysis
Pattern Recognition, Automated
Reproducibility of Results
Robotics
Sensitivity and Specificity
Sequence Analysis, DNA