Citation
Izquierdo-García, Jose L. and Rodriguez, Ignacio and Kyriazis, Angelos and Villa, Palmira and Barreiro Elorza, Pilar and Desco, Manuel and Ruiz Cabello Osuna, Jesus Maria
(2009).
A novel R-package graphic user interface for the analysis of metabonomic profiles.
"BMC Informatics", v. 10
;
pp. 1-10.
ISSN 1471-2105.
https://doi.org/10.1186/1471-2105-10-363.
Abstract
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.