PLS/OPLS models in metabolomics: the impact of permutation of dataset rows on the K-fold cross-validation quality parameters
2015
Triba, Mohamed N. | Le Moyec, Laurence | Amathieu, Roland | Goossens, Corentine | Bouchemal, Nadia | Nahon, Pierre | Rutledge, Douglas N. | Savarin, Philippe | Chimie, Structures et Propriétés de Biomatériaux et d'Agents Thérapeutiques (CSPBAT) ; Université Paris 13 (UP13)-Institut Galilée-Université Sorbonne Paris Cité (USPC)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS) | Unité de biologie intégrative des adaptations à l'exercice (UBIAE) ; Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Santé et de la Recherche Médicale (INSERM) | Service d'Anesthésie et des Réanimations Chirurgicales ; Centre Hospitalier Universitaire Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12) | Service d'Hépatologie ; Université Paris 13 (UP13)-Hôpital Jean Verdier [AP-HP] ; Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP) | Ingénierie, Procédés, Aliments (GENIAL) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech
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, Umea 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, R-2, Q(2), PCV-ANOVA, and the permutation test). Significance thresholds for these parameters are strongly application-dependent. Concerning the Q(2) 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 Q(2) 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 Q(2) 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.
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