Genetic algorithm based two-mode clustering of metabolomics data

Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of subsets of metabolites under different experimental conditions. In addition, the results are easily visualized. In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets. It was, for instance, able to identify a catabolic pathway for growth on several of the carbon sources

Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data

Longitudinal intervention studies with repeated measurements over time are an important type of experimental design in biomedical research. Due to the advent of “omics”-sciences (genomics, transcriptomics, proteomics, metabolomics), longitudinal studies generate increasingly multivariate outcome data. Analysis of such data must take both the longitudinal intervention structure and multivariate nature of the data into account. The ASCA+-framework combines general linear models with principal component analysis and can be used to separate and visualize the multivariate effect of different experimental factors. However, this methodology has not yet been developed for the more complex designs often found in longitudinal intervention studies, which may be unbalanced, involve randomized interventions, and have substantial missing data. Here we describe a new methodology, repeated measures ASCA+ (RM-ASCA+), and show how it can be used to model metabolic changes over time, and compare metabolic changes between groups, in both randomized and non-randomized intervention studies. Tools for both visualization and model validation are discussed. This approach can facilitate easier interpretation of data from longitudinal clinical trials with multivariate outcomes

Orthogonality constrained inverse regression to improve model selectivity and analyte predictions from vibrational spectroscopic measurements

In analytical chemistry spectroscopy is attractive for high-throughput quantification, which often relies on inverse regression, like partial least squares regression. Due to a multivariate nature of spectroscopic measurements an analyte can be quantified in presence of interferences. However, if the model is not fully selective against interferences, analyte predictions may be biased. The degree of model selectivity against an interferent is defined by the inner relation between the regression vector and the pure interfering signal. If the regression vector is orthogonal to the signal, this inner relation equals zero and the model is fully selective. The degree of model selectivity largely depends on calibration data quality. Strong correlations may deteriorate calibration data resulting in poorly selective models. We show this using a fructose-maltose model system. Furthermore, we modify the NIPALS algorithm to improve model selectivity when calibration data are deteriorated. This modification is done by incorporating a projection matrix into the algorithm, which constrains regression vector estimation to the null-space of known interfering signals. This way known interfering signals are handled, while unknown signals are accounted for by latent variables. We test the modified algorithm and compare it to the conventional NIPALS algorithm using both simulated and industrial process data. The industrial process data consist of mid-infrared measurements obtained on mixtures of beta-lactoglobulin (analyte of interest), and alpha-lactalbumin and caseinoglycomacropeptide (interfering species). The root mean squared error of beta-lactoglobulin (% w/w) predictions of a test set was 0.92 and 0.33 when applying the conventional and the modified NIPALS algorithm, respectively. Our modification of the algorithm returns simpler models with improved selectivity and analyte predictions. This paper shows how known interfering signals may be utilized in a direct fashion, while benefitting from a latent variable approach. The modified algorithm can be viewed as a fusion between ordinary least squares regression and partial least squares regression and may be very useful when knowledge of some (but not all) interfering species is available