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Open Access Highly Accessed Software

K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space

Max Bylesjö1, Mattias Rantalainen2, Jeremy K Nicholson2, Elaine Holmes2 and Johan Trygg1*

Author Affiliations

1 Research Group for Chemometrics, Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden

2 Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College, London, SW7 2AZ, UK

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BMC Bioinformatics 2008, 9:106  doi:10.1186/1471-2105-9-106

Published: 19 February 2008

Abstract

Background

Kernel-based classification and regression methods have been successfully applied to modelling a wide variety of biological data. The Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method offers unique properties facilitating separate modelling of predictive variation and structured noise in the feature space. While providing prediction results similar to other kernel-based methods, K-OPLS features enhanced interpretational capabilities; allowing detection of unanticipated systematic variation in the data such as instrumental drift, batch variability or unexpected biological variation.

Results

We demonstrate an implementation of the K-OPLS algorithm for MATLAB and R, licensed under the GNU GPL and available at http://www.sourceforge.net/projects/kopls/ webcite. The package includes essential functionality and documentation for model evaluation (using cross-validation), training and prediction of future samples. Incorporated is also a set of diagnostic tools and plot functions to simplify the visualisation of data, e.g. for detecting trends or for identification of outlying samples. The utility of the software package is demonstrated by means of a metabolic profiling data set from a biological study of hybrid aspen.

Conclusion

The properties of the K-OPLS method are well suited for analysis of biological data, which in conjunction with the availability of the outlined open-source package provides a comprehensive solution for kernel-based analysis in bioinformatics applications.