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}, local-url = {file://localhost/Users/jruizcabello/Documents/JRC/biblio/Papers-folder/Library.papers3/Files/3A/3A68F8DD-2381-4092-B0BF-87845EFE84D7.pdf}, file = {{3A68F8DD-2381-4092-B0BF-87845EFE84D7.pdf:/Users/jruizcabello/Documents/JRC/biblio/Papers-folder/Library.papers3/Files/3A/3A68F8DD-2381-4092-B0BF-87845EFE84D7.pdf:application/pdf}}, uri = {url{papers3://publication/doi/10.1186/1471-2105-10-363}} }