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

Radka Stoyanova·Troy D Querec·Truman R Brown·Christos Patriotis
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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.

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AlgorithmsComputer SimulationEpitheliumFemaleGene Expression ProfilingGene Expression RegulationHumansModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisOvaryPrincipal Component AnalysisReproducibility of ResultsSensitivity and SpecificityComparative StudyEvaluation StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.Validation Study

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Radka Stoyanova, Troy D Querec, Truman R Brown, Christos Patriotis. 2004-03-22. Normalization of single-channel DNA array data by principal component analysis.. https://doi.org/10.1093/bioinformatics%2Fbth170

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