A novel R-package graphic user interface for the analysis of metabonomic profiles

Background Analysis of the plethora of metabolites found in the NMR spectra of biological fluids or tissues requires data complexity to be simplified. We present a graphical user interface (GUI) for NMR-based metabonomic analysis. The "Metabonomic Package" has been developed for metabonomics research as open-source software and uses the R statistical libraries. /Results The package offers the following options: Raw 1-dimensional spectra processing: phase, baseline correction and normalization. Importing processed spectra. Including/excluding spectral ranges, optional binning and bucketing, detection and alignment of peaks. Sorting of metabolites based on their ability to discriminate, metabolite selection, and outlier identification. Multivariate unsupervised analysis: principal components analysis (PCA). Multivariate supervised analysis: partial least squares (PLS), linear discriminant analysis (LDA), k-nearest neighbor classification. Neural networks. Visualization and overlapping of spectra. Plot values of the chemical shift position for different samples. Furthermore, the "Metabonomic" GUI includes a console to enable other kinds of analyses and to take advantage of all R statistical tools. /Conclusion We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics

Partial least squares discriminant analysis: A dimensionality reduction method to classify hyperspectral data

The recent development of more sophisticated spectroscopic methods allows acquisition of high dimensional datasets from which valuable information may be extracted using multivariate statistical analyses, such as dimensionality reduction and automatic classification (supervised and unsupervised). In this work, a supervised classification through a partial least squares discriminant analysis (PLS-DA) is performed on the hy- perspectral data. The obtained results are compared with those obtained by the most commonly used classification approaches

Partial least squares discriminant analysis: A dimensionality reduction method to classify hyperspectral data

The recent development of more sophisticated spectroscopic methods allows acqui- sition of high dimensional datasets from which valuable information may be extracted using multivariate statistical analyses, such as dimensionality reduction and automatic classification (supervised and unsupervised). In this work, a supervised classification through a partial least squares discriminant analysis (PLS-DA) is performed on the hy- perspectral data. The obtained results are compared with those obtained by the most commonly used classification approaches

Discriminant Analysis with Spatial Weights for Urban Land Cover Classification

Classifying urban area images is challenging because of the heterogeneous nature of the urban landscape resulting in mixed pixels and classes with highly variable spectral ranges. Approaches using ancillary data, such as knowledge based or expert systems, have shown to improve the classification accuracy in urban areas. Appropriate ancillary data, however, may not always be available. The goal of this study is to compare the results of the discriminant analysis statistical technique with discriminant analysis with spatial weights to classify urban land cover. Discriminant analysis is a statistical technique used to predict group membership for a target based on the linear combination of independent variables. Strict per pixel statistical analysis however does not consider the spatial dependencies among neighbouring pixels. Our study shows that approaches using ancillary data continue to outperform strict spectral classifiers but that using a spatial weight improved the results. Furthermore, results show that when the discriminant analysis technique works well then the spatially weighted approach performs better. However, when the discriminant analysis performs poorly, those poor results are magnified in the spatially weighted approach in the same study area. The study shows that for dominant classes, adding spatial weights improves the classification accuracy.