Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

Publication

Stability of gene contributions and identification of outliers in multivariate analysis of microarray data

Journal Paper/Review - Jan 1, 2008

Baty Florent, Jaeger Daniel, Preiswerk Frank, Schumacher Martin M, Brutsche Martin

Citation

Baty F, Jaeger D, Preiswerk F, Schumacher M, Brutsche M. Stability of gene contributions and identification of outliers in multivariate analysis of microarray data. BMC bioinformatics 2008; 9:289.

Type

Journal Paper/Review (English)

Journal

BMC bioinformatics 2008; 9

Publication Date

Jan 1, 2008

Issn Electronic

1471-2105

Pages

289

Brief description/objective

BACKGROUND: Multivariate ordination methods are powerful tools for the exploration of complex data structures present in microarray data. These methods have several advantages compared to common gene-by-gene approaches. However, due to their exploratory nature, multivariate ordination methods do not allow direct statistical testing of the stability of genes. RESULTS: In this study, we developed a computationally efficient algorithm for: i) the assessment of the significance of gene contributions and ii) the identification of sample outliers in multivariate analysis of microarray data. The approach is based on the use of resampling methods including bootstrapping and jackknifing. A statistical package of R functions was developed. This package includes tools for both inferring the statistical significance of gene contributions and identifying outliers among samples. CONCLUSION: The methodology was successfully applied to three published data sets with varying levels of signal intensities. Its relevance was compared with alternative methods. Overall, it proved to be particularly effective for the evaluation of the stability of microarray data.