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A randomization test for PLS component selection
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Research Group for Chemometrics)
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Research Group for Chemometrics)
Umetrics, Umeå, Sweden.
Umeå University, Faculty of Science and Technology, Department of Chemistry. (Research Group for Chemometrics)
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2007 (English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 21, no 10-11, 427-439 p.Article in journal (Refereed) Published
Abstract [en]

During the last two decades, a number of methods have been developed and evaluated for selecting the optimal number of components in a PLS model. In this paper, a new method is introduced that is based on a randomization test. The advantage of using a randomization test is that in contrast to cross validation (CV), it requires no exclusion of data, thus avoiding problems related to data exclusion, for example in designed experiments. The method is tested using simulated data sets for which the true dimensionality is clearly defined and also compared to regularly used methods for 10 real data sets. The randomization test works as a good statistical selection tool in combination with other selection rules. It also works as an indicator when the data require a pre-treatment.

Place, publisher, year, edition, pages
Chichester: Wiley & Sons , 2007. Vol. 21, no 10-11, 427-439 p.
Keyword [en]
randomization test, permutation test, component selection, factor selection, latent variable selection
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:umu:diva-2653DOI: 10.1002/cem.1086OAI: oai:DiVA.org:umu-2653DiVA: diva2:140880
Available from: 2007-10-19 Created: 2007-10-19 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Spectroscopic data and multivariate analysis: tools to study genetic perturbations in poplar trees
Open this publication in new window or tab >>Spectroscopic data and multivariate analysis: tools to study genetic perturbations in poplar trees
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In our society in the 21st century one of the greatest challenges is to provide raw materials to the industry in a sustainable way. This requires increased use of renewable raw materials such as wood. Wood is widely used in pulp, paper and textile industries and ongoing research efforts aim to extend the use of wood in e.g. liquid biofuels and green chemicals. At Umeå Plant Science Center (UPSC) poplar trees are used as model systems to study wood formation. The objective is to understand the function of the genes underlying the wood forming process. This knowledge could result in improved chemical and physical wood properties suitable for different industrial processes. This will in turn meet the demands for a sustainable development.

This thesis presents tools and strategies to unravel information regarding genetic perturbations in poplar trees by the use of nuclear magnetic resonance (NMR) spectroscopy and multivariate analysis (MVA). Furthermore, gas chromatography/mass spectrometry (GC/MS) is briefly discussed in this context. Multivariate methods to find patterns and trends in NMR data have been used for more than 30 years. In the beginning MVA was applied in pattern recognition studies in order to characterize chemical structures with different ligands and in different solvents. Today, the multivariate methods have developed and the research have changed focus towards the study of biofluids from plant extracts, urine, blood plasma, saliva etc. NMR spectra of biofluids can contain thousands of resonances, originating from hundreds of different compounds. This type of complex data can be hard to summarize and interpret without appropriate tools and require sophisticated strategies for data evaluation. Related fields of research are rapidly growing and are here referred to as metabolomics.

Five different research projects are presented which includes analysis of poplar samples where macromolecules such as pectin and also small molecules such as metabolites were analysed by high resolution magic angle spinning (HR/MAS) NMR spectroscopy, 1H-13C HSQC NMR and GC/MS. The discussion topics include modelling of metabolomic time dependencies in combination with genetic variation, validation of orthogonal projections to latent structures (OPLS) models, selection of putative biomarkers related to genetic modification from OPLS-discriminant analysis (DA) models, measuring one of the main components found in the primary cell-walls of poplar i.e. pectin, the use of Fourier transformed two-dimensional (2D) NMR data in OPLS modelling and model complexity in a PLS model.

Place, publisher, year, edition, pages
Umeå: Kemi, 2007. 81 p.
Keyword
NMR spectroscopy, Metabolomics, Degree of methylation, S-plot, SUS-plot, Metabonomics, Poplar, MLR, PLS, OPLS, PCA, Pectin, Wood
National Category
Organic Chemistry
Identifiers
urn:nbn:se:umu:diva-1396 (URN)978-91-7264-380-2 (ISBN)
Public defence
2007-11-09, N360, Johan bures väg, Umeå, 10:00
Opponent
Supervisors
Available from: 2007-10-19 Created: 2007-10-19 Last updated: 2011-04-21Bibliographically approved

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