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Nucleic Acids Research, 2000, Vol. 28, No. 22 4577-4581
© 2000 Oxford University Press

Quantitative analysis of DNA array autoradiographs

Charles A. Pelizzari*, Nikolai N. Khodarev, Nalin Gupta, Douglas P. Calvin and Ralph R. Weichselbaum

Department of Radiation and Cellular Oncology, The University of Chicago, 5841 South Maryland Avenue, MC 9006 Chicago, IL 60637, USA

DNA arrays and chips are powerful new tools for gene expression profiling. Current arrays contain hundreds or thousands of probes and large scale sequencing and screening projects will likely lead to the creation of global genomic arrays. DNA arrays and chips will be key in understanding how genes respond to specific changes of environment and will also greatly assist in drug discovery and molecular diagnostics. To facilitate widespread realization of the quantitative potential of this approach, we have designed procedures and software which facilitate analysis of autoradiography films with accuracy comparable to phosphorimaging devices. Algorithms designed for analysis of DNA array autoradiographs incorporate 3-D peak fitting of features on films and estimation of local backgrounds. This software has a flexible grid geometry and can be applied to different types of DNA arrays, including custom arrays.

* To whom correspondence should be addressed. Tel: +1 773 702 6841; Fax: +1 773 834 7299; Email: c-pelizzari{at}uchicago.edu


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