Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 2.3.14
Date: 2018-08-16
Author: Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
Email: etienne.thevenot(at)cea.fr
Citation: 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
Licence: CeCILL
Reference history: W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine_complete
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

Installation

• Configuration file: multivariate_config.xml
• Image files:
  • static/images/multivariate_workflowPositionImage.png
  • static/images/multivariate_workingExampleImage.png
• Wrapper file: multivariate_wrapper.R

• R packages

  • batch from CRAN

  install.packages("batch", dep=TRUE)  

  • ropls from Bioconductor

  source("http://www.bioconductor.org/biocLite.R")  
  biocLite("ropls")      

Tests

The code in the wrapper can be tested by running the runit/multivariate_runtests.R R file

You will need to install RUnit package in order to make it run:

install.packages('RUnit', dependencies = TRUE)

Working example

See the W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine-subset-complete, W4M00002_mtbls2, W4M00003_diaplasma shared histories in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)

News

CHANGES IN VERSION 2.3.14

MINOR CORRECTION

• Score plot (x-score) advanced parameters (labels and colors) in case of test samples in the dataset

CHANGES IN VERSION 2.3.12

NEW FEATURE

• Some of the parameters were renamed according to the controlled vocabulary of the Ontology for Biomedical Investigations (OBI; http://obi-ontology.org/) and the statistics ontology (STATO; http://stato-ontology.org/), in collaboration with Philippe Rocca-Serra (University of Oxford)

CHANGES IN VERSION 2.3.8

MINOR MODIFICATION

• (O)PLS(-DA) coefficients display in case of multiple quantitative (or multiclass) response: now the column names of the coefficients for each response are correctly labelled in the variableMetadata file

CHANGES IN VERSION 2.3.6

INTERNAL MODIFICATION

• minor internal modifications

CHANGES IN VERSION 2.3.4

INTERNAL MODIFICATION

• minor update of .shed.yml

CHANGES IN VERSION 2.3.2

INTERNAL MODIFICATION

• Modification of the multivariate_wrapper.R file to handle ropls package versions of 1.3.15 and above (i.e. after switching to S4 classes)

CHANGES IN VERSION 2.3.0

NEW FEATURES

• Predictions now available (see the 'Samples to be tested' argument)
• OPLS(-DA): Predictive and Orthogonal VIP are now computed (see the 'comments' section)
• Multiclass PLS-DA implemented (see the 'comments' section)