Normalization of single-channel DNA array data by principal component analysis.
BACKGROUND
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.
Stoyanova
Radka
R
Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111-2497, USA.
Querec
Troy D
TD
Brown
Truman R
TR
Patriotis
Christos
C
D000465:Algorithms; D003198:Computer Simulation; D004848:Epithelium / Q000502:physiology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D005786:Gene Expression Regulation / Q000502:physiology; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D010053:Ovary / Q000502:physiology; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity