Biostatistics

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.

BACKGROUND:

In metabolomics research a large number of metabolites are measured that reflect the cellular state under the experimental conditions studied. In many occasions the experiments are performed according to an experimental design to make sure that sufficient variation is induced in the metabolite concentrations. However, as metabolomics is a holistic approach, also a large number of metabolites are measured in which no variation is induced by the experimental design.

Many benefits can be gained if multi-factorial diseases with a high incidence and prevalence are better understood. Sophisticated approaches like multilevel analyses are needed to discover subtle differences between healthy people and people at the onset of disease in these types of studies. Multilevel analysis generates different sub-models for each level of variation. For instance, within and between subject variation can be split and analyzed separately if the two factors are orthogonal (i.e., not confounded).

In metabolomics, time-resolved, dynamic or temporal data is more and more collected. The number of methods to analyze such data, however, is very limited and in most cases the dynamic nature of the data is not even taken into account. This paper reviews current methods in use for analyzing dynamic metabolomic data. Moreover, some methods from other fields of science that may be of use to analyze such dynamic metabolomics data are described in some detail. The methods are put in a general framework after providing a formal definition on what constitutes a 'dynamic' method.