by Izquierdo-García, José L, Rodriguez, Ignacio, Kyriazis, Angelos, Villa, Palmira, Barreiro, Pilar, Desco, Manuel and Ruiz-Cabello, Jesus
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.
Reference:
A novel R-package graphic user interface for the analysis of metabonomic profiles. (Izquierdo-García, José L, Rodriguez, Ignacio, Kyriazis, Angelos, Villa, Palmira, Barreiro, Pilar, Desco, Manuel and Ruiz-Cabello, Jesus), In BMC bioinformatics, BioMed Central, volume 10, 2009.
Bibtex Entry:
@article{IzquierdoGarcia:2009hdd,
author = {Izquierdo-Garc{'i}a, Jos{'e} L and Rodriguez, Ignacio and Kyriazis, Angelos and Villa, Palmira and Barreiro, Pilar and Desco, Manuel and Ruiz-Cabello, Jesus},
title = {{A novel R-package graphic user interface for the analysis of metabonomic profiles.}},
journal = {BMC bioinformatics},
year = {2009},
volume = {10},
number = {1},
pages = {363},
month = oct,
publisher = {BioMed Central},
affiliation = {Instituto de Estudios Biofuncionales, UCM, Madrid, Spain. izquierdo@ieb.ucm.es},
doi = {10.1186/1471-2105-10-363},
pmid = {19874601},
pmcid = {PMC2774703},
language = {English},
rating = {0},
date-added = {2018-03-16T12:39:59GMT},
date-modified = {2020-07-09T13:27:51GMT},
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.},
url = {http://www.biomedcentral.com/1471-2105/10/363},
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