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


CONCLUSIONS
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.
Pulmonary Gene Research, University Hospital Basel, Petersgraben 4, Basel, Switzerland. florent.baty@unibas.ch
Florent
F
Baty
Daniel
D
Jaeger
Frank
F
Preiswerk
Martin M
MM
Schumacher
Martin H
MH
Brutsche
D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D042822:Genomic Instability / Q000235:genetics*; D015999:Multivariate Analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020543:Proteome / Q000235:genetics*
D020543:Proteome