Visit of Laboratory for ChemoMetrics, Vienna (Austria):      18 November 2010

 

Ron Wehrens

Centro Ricerca e Innovazione, Fondazione Edmund Mach

Istituto Agrario di San Michele all'Adige, Italy

www.iasma.it

 

Kurt Varmuza                                                           Ron Wehrens

 

 

 

Seminar lecture by Ron Wehrens* at Institute of Statistics and Probability Theory,

Vienna University of Technology (invited by Peter Filzmoser)

 

17 November 2010

 

Biomarker identification in metabolomics

Abstract

Knowledge on which metabolites are indicative of class differences is important for a better understanding of underlying biological processes. To achieve this, several approaches can be used. Among the most popular are the strategies based on PLSDA, either by assessing the absolute size of the model coefficients or by looking at derived statistics such as the variable-importance measure. These necessitate some form of validation, in order to determine the optimal number of latent variables. Univariate statistics based on t-tests are potentially simpler to apply but still need appropriate cut-off points, and cannot use correlation information.

We discuss an alternative strategy for biomarker discovery, based on the stability of the candidate biomarker set under perturbance of the data. We evaluate the performance of these using a real LCMS data set obtained by spiking apple extracts with known metabolites at different concentrations, in order to mimic real-life experimental conditions.

The scope of the data has been extended by using these apple data for simulations of much larger data sets with similar characteristics. In this way, we can assess the effect of the variable-to-sample ratio on the biomarker identification, which in metabolomics usually is quite large.

This is based on joint work with Pietro Franceschi, Urska Vrhovsek and Fulvio Mattivi.

 

* Ron Wehrens obtained a PhD in Chemometrics at the Radboud University Nijmegen, The Netherlands. He was a lecturer in Analytical Chemistry at the University of Twente, and later an associated professor at the Radboud University Nijmegen. Since January 2010, he is group leader in Biostatistics and Data Analysis at the Fondazione Edmund Mach in San Michele all'Adige, Italy.

 

New book will be published soon <link>:

Wehrens R.: Chemometrics with R, Springer (Berlin)

 

 

 

 

 

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