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Bioinformatics Advance Access originally published online on March 22, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Normalization of single-channel DNA array data by principal component analysis

Radka Stoyanova 1, Troy D. Querec 2,{dagger}, Truman R. Brown 3 and Christos Patriotis 2,*

1 Division of Population Science and 2 Department of Medical Oncology, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497 and 3 Hatch Center for MR Research, Columbia University, 710 W. 168th St., New York, NY 10032, USA

Received on July 9, 2003; revised on January 8, 2004; accepted on February 8, 2004
Advance Access Publication March 22, 2004

Motivation: Detailed comparison and analysis of the output of DNA gene expression arrays from multiple samples require global normalization of the measured individual gene intensities from the different hybridizations. This is needed for accounting for variations in array preparation and sample hybridization conditions.

Results: Here, we present a simple, robust and accurate procedure for the global normalization of datasets generated with single-channel DNA arrays based on principal component analysis. The procedure makes minimal assumptions about the data and performs well in cases where other standard procedures produced biased estimates. It is also insensitive to data transformation, filtering (thresholding) and pre-screening.

Contact: Christos.Patriotis{at}fccc.edu

* To whom correspondence should be addressed.

{dagger} Present address: Emory University, GDBBS, 1462 Clifton Road, Dental Bldg, Suite 314, Atlanta, GA 30322, USA.


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