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Bioinformatics Advance Access published online on March 25, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth188
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 9, 2003
Revised January 29, 2004
Accepted February 8, 2004

Article

A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays

Troy D. Querec 1, Radka Stoyanova 2, Eric Ross 3, Christos Patriotis 1*

1 Department of Medical Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497
2 Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497
3 Department of Biostatistics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497

* To whom correspondence should be addressed. E-mail: C_Patriotis{at}fccc.edu.


  Abstract

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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