Open Access Open Badges Research article

Statistical validation of megavariate effects in ASCA

Daniel J Vis1*, Johan A Westerhuis1, Age K Smilde12 and Jan van der Greef2

Author Affiliations

1 BioSystems Data Analysis group, Swammerdam Institute for Life Science, University of Amsterdam, The Netherlands

2 TNO Quality of Life, Zeist, The Netherlands

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BMC Bioinformatics 2007, 8:322  doi:10.1186/1471-2105-8-322

Published: 30 August 2007



Innovative extensions of (M) ANOVA gain common ground for the analysis of designed metabolomics experiments. ASCA is such a multivariate analysis method; it has successfully estimated effects in megavariate metabolomics data from biological experiments. However, rigorous statistical validation of megavariate effects is still problematic because megavariate extensions of the classical F-test do not exist.


A permutation approach is used to validate megavariate effects observed with ASCA. By permuting the class labels of the underlying experimental design, a distribution of no-effect is calculated. If the observed effect is clearly different from this distribution the effect is deemed significant


The permutation approach is studied using simulated data which gave successful results. It was then used on real-life metabolomics data set dealing with bromobenzene-dosed rats. In this metabolomics experiment the dosage and time-interaction effect were validated, both effects are significant. Histological screening of the treated rats' liver agrees with this finding.


The suggested procedure gives approximate p-values for testing effects underlying metabolomics data sets. Therefore, performing model validation is possible using the proposed procedure.