"Sacurine-statistics" history (W4M00001)

Workflow4Metabolomics Object Identifier: W4M00001

Digital Object Identifier: 10.15454/1.4811121736910142E12

Creator of the history: Etienne Thévenot

Maintainer: Etienne Thévenot (etienne.thevenot at cea.fr)

Creation|Updating date: 2015-06-19

Format: Workflow4Metabolomics Galaxy histories

W4M History: https://galaxy.workflow4metabolomics.org/history/list_published

Size:  4 Mo

Keywords: age, bmi, gender, homosapiens, urine, lcms and statistics

Description:

Study: Characterization of the physiological variations of the metabolome in biofluids is critical to understand human physiology and to avoid confounding effects in cohort studies aiming at biomarker discovery. @w4m
Dataset: In this study conducted by the MetaboHUB French Infrastructure for Metabolomics, urine samples from 184 volunteers were analyzed by reversed-phase (C18) ultrahigh performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (LTQ-Orbitrap). A total of 258 metabolites were identified at confidence levels provided by the metabolomics standards initiative (MSI) levels 1 or 2.
Workflow: This history describes the statistical analysis of the data set from the negative ionization mode (113 identified metabolites at MSI levels 1 or 2): correction of signal drift (loess model built on QC pools) and batch effects (two batches), variable filtering (QC coefficent of variation < 30%), normalization by the sample osmolality, log10 transformation, sample filtering (Hotelling, decile and missing pvalues > 0.001) resulting in the HU_096 sample being discarded, univariate hypothesis testing of significant variations with age, BMI, or between genders (FDR < 0.05), and OPLS(-DA) modeling of age, BMI and gender.

Comments: The ‘sacurine’ data set (after normalization and filtering) is also available in the ropls R package from the Bioconductor repository. For a comprehensive analysis of the dataset (starting from the preprocessing of the raw files and including all detected features in the subsequent steps), please see the companion ‘W4M00002_Sacurine-comprehensive’ reference history.

 Rights:  Creative Commons

Citations:

  • Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. Journal of Proteome Research, 14:3322-3335. DOI:10.1021/acs.jproteome.5b00354

Raw data repository

 

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