Assessment of PLSDA cross validation

作者：Johan A. Westerhuis, Huub C. J. Hoefsloot, Suzanne Smit, Daniël J. Vis, Age K. Smilde, Ewoud J. J. van Velzen, John van Duynhoven, Ferdi A. van Dorsten · 发表于：Metabolomics · 年份：2008 · DOI：10.1007/s11306-007-0099-6 · 被引用次数：1488 · 研究领域：Metabolomics and Mass Spectrometry Studies、Computational Drug Discovery Methods、Spectroscopy and Chemometric Analyses

Classifying groups of individuals based on their metabolic profile is one of the main topics in metabolomics research. Due to the low number of individuals compared to the large number of variables, this is not an easy task. PLSDA is one of the data analysis methods used for the classification. Unfortunately this method eagerly overfits the data and rigorous validation is necessary. The validation however is far from straightforward. Is this paper we will discuss a strategy based on cross model validation and permutation testing to validate the classification models. It is also shown that too optimistic results are obtained when the validation is not done properly. Furthermore, we advocate against the use of PLSDA score plots for inference of class differences.