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

• Main Authors: Villa Palmira, Kyriazis Angelos, Rodríguez Ignacio, Izquierdo-García Jose L, Barreiro Pilar, Desco Manuel, Ruiz-Cabello Jesús
• Format: Article
• Language: English
• Published: BMC 2009-10-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/10/363

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>The package offers the following options:</p> <p>Raw 1-dimensional spectra processing: phase, baseline correction and normalization.</p> <p>Importing processed spectra.</p> <p>Including/excluding spectral ranges, optional binning and bucketing, detection and alignment of peaks.</p> <p>Sorting of metabolites based on their ability to discriminate, metabolite selection, and outlier identification.</p> <p>Multivariate unsupervised analysis: principal components analysis (PCA).</p> <p>Multivariate supervised analysis: partial least squares (PLS), linear discriminant analysis (LDA), k-nearest neighbor classification.</p> <p>Neural networks.</p> <p>Visualization and overlapping of spectra.</p> <p>Plot values of the chemical shift position for different samples.</p> <p>Furthermore, the "Metabonomic" GUI includes a console to enable other kinds of analyses and to take advantage of all R statistical tools.</p> <p>Conclusion</p> <p>We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics.</p>