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

  • Authors:

  • Radka Stoyanova;Troy D. Querec;Truman R. Brown;Christos Patriotis

  • Affiliations:

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

  • Venue:
  • Bioinformatics
  • Year:
  • 2004

Quantified Score

Hi-index 3.84

Visualization

Abstract

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.