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.


CONCLUSIONS
We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics.
Izquierdo-García
Jose L
JL
Instituto de Estudios Biofuncionales, UCM, Madrid, Spain. izquierdo@ieb.ucm.es
Rodríguez
Ignacio
I
Kyriazis
Angelos
A
Villa
Palmira
P
Barreiro
Pilar
P
Desco
Manuel
M
Ruiz-Cabello
Jesús
J
D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D016002:Discriminant Analysis; D055432:Metabolomics / Q000379:methods*; D025341:Principal Component Analysis; D012984:Software; D014584:User-Computer Interface