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

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.

Description

Title: A novel R-package graphic user interface for the analysis of metabonomic profiles
Author/s:
  • Izquierdo-García, Jose L.
  • Rodriguez, Ignacio
  • Kyriazis, Angelos
  • Villa, Palmira
  • Barreiro Elorza, Pilar
  • Desco, Manuel
  • Ruiz Cabello Osuna, Jesus Maria
Item Type: Article
Título de Revista/Publicación: BMC Informatics
Date: October 2009
ISSN: 1471-2105
Volume: 10
Subjects:
Faculty: E.T.S.I. Agrónomos (UPM) [antigua denominación]
Department: Ingeniería Rural [hasta 2014]
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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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.

More information

Item ID: 5026
DC Identifier: http://oa.upm.es/5026/
OAI Identifier: oai:oa.upm.es:5026
DOI: 10.1186/1471-2105-10-363
Official URL: http://www.biomedcentral.com/1471-2105/10/363
Deposited by: Memoria Investigacion
Deposited on: 19 Nov 2010 08:59
Last Modified: 20 Apr 2016 14:00
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