Publication

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

Journal Paper/Review - Jan 1, 2008

Units
PubMed
Doi

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.