Bioinformatics Advance Access originally published online on March 25, 2004
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Bioinformatics 20(12) © Oxford University Press 2004; all rights reserved.
A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays
1 Department of Medical Oncology, 2 Division of Population Science and 3 Department of Biostatistics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497, USA
Received on July 9, 2003; revised on January 29, 2004; accepted on February 8, 2004
Advance Access Publication March 25, 2004
Motivation: The radioactivity labeled DNA array platform is a robust and accurate way for a high-throughput measurement of gene expression levels in biological samples. Despite its high degree of sensitivity and reproducibility, this platform has several sources of variation. These are related to the presence of saturation effects in the array images and impede the degree of accuracy at which gene expression levels are determined.
Results: Here we describe a simple, but effective, approach for combining expression data from a series of autoradiographic exposures of variable length. This technique increases the sensitivity of this array platform by detecting low-expressed genes at longer exposures. It also improves the measurement accuracy of highly abundant genes by considering only values from the linear portion of dependency between the exposure times and gene intensities. As a result, the described approach improves the outcome of the subsequent steps of array data normalization and mining.
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Present address: Emory University, GDBBS, 1462 Clifton Road, Dental Building, Suite 314, Atlanta, GA 30322, USA