NDLI: PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Triba, Mohamed N. Le Moyec, Laurence Amathieu, Roland Goossens, Corentine Bouchemal, Nadia Nahon, Pierre Rutledge, Douglas N. Savarin, Philippe
Description	Country affiliation: France Author Affiliation: Triba MN ( Université Paris 13, Sorbonne Paris Cité, Laboratoire Chimie, Structures, Propriétés de Biomatériaux et d'Agents Thérapeutiques (CSPBAT), Unité Mixte de Recherche (UMR) 7244, Centre National de Recherche Scientifique (CNRS), Equipe Spectroscopie des Biomolécules et des Milieux Biologiques (SBMB), 74 rue Marcel Cachin, 93037, Bobigny, France. mohamed.triba@univ-paris13.fr.)
Abstract	Among all the software packages available for discriminant analyses based on projection to latent structures (PLS-DA) or orthogonal projection to latent structures (OPLS-DA), SIMCA (Umetrics, Umeå Sweden) is the more widely used in the metabolomics field. SIMCA proposes many parameters or tests to assess the quality of the computed model (the number of significant components, R2, Q2, pCV-ANOVA, and the permutation test). Significance thresholds for these parameters are strongly application-dependent. Concerning the Q2 parameter, a significance threshold of 0.5 is generally admitted. However, during the last few years, many PLS-DA/OPLS-DA models built using SIMCA have been published with Q2 values lower than 0.5. The purpose of this opinion note is to point out that, in some circumstances frequently encountered in metabolomics, the values of these parameters strongly depend on the individuals that constitute the validation subsets. As a result of the way in which the software selects members of the calibration and validation subsets, a simple permutation of dataset rows can, in several cases, lead to contradictory conclusions about the significance of the models when a K-fold cross-validation is used. We believe that, when Q2 values lower than 0.5 are obtained, SIMCA users should at least verify that the quality parameters are stable towards permutation of the rows in their dataset.
File Format	HTM / HTML
ISSN	1742206X
Issue Number	1
Volume Number	11
e-ISSN	17422051
Journal	Molecular BioSystems
Language	English
Publisher	Royal Society of Chemistry
Publisher Date	2015-01-01
Publisher Place	Great Britain (UK)
Access Restriction	Subscribed
Subject Keyword	Discipline Molecular Biology Discipline Biochemistry Metabolomics Methods Models, Statistical Software Humans Mutation Reproducibility Of Results Journal Article Review
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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