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Biologically valid linear factor models of gene expression

Girolami, M; Breitling, R; (2004) Biologically valid linear factor models of gene expression. BIOINFORMATICS , 20 (17) 3021 - 3033. 10.1093/bioinformatics/bth354.

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Abstract

Motivation: The identification of physiological processes underlying and generating the expression pattern observed in microarray experiments is a major challenge. Principal component analysis (PCA) is a linear multivariate statistical method that is regularly employed for that purpose as it provides a reduced-dimensional representation for subsequent study of possible biological processes responding to the particular experimental conditions. Making explicit the data assumptions underlying PCA highlights their lack of biological validity thus making biological interpretation of the principal components problematic. A microarray data representation which enables clear biological interpretation is a desirable analysis tool.Results: We address this issue by employing the probabilistic interpretation of PCA and proposing alternative linear factor models which are based on refined biological assumptions. A practical study on two well-understood microarray datasets highlights the weakness of PCA and the greater biological interpretability of the linear models we have developed.

Type:Article
Title:Biologically valid linear factor models of gene expression
DOI:10.1093/bioinformatics/bth354
Keywords:PRINCIPAL COMPONENT ANALYSIS, DECOMPOSITION, IDENTIFICATION, CLASSIFICATION, PROFILES, CANCER, CELLS
UCL classification:UCL > School of BEAMS > Faculty of Maths and Physical Sciences > Statistical Science

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