workflow4metabolomics/batch_correction

Name: batch_correction

Owner: Workflow4Metabolomics

Description: Correction for signal drift and batch effects

Created: 2017-02-28 13:44:12.0

Updated: 2017-02-28 13:48:49.0

Pushed: 2017-12-14 15:07:57.0

Homepage: null

Size: 9952

Language: R

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README

Signal drift and batch-effect correction

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 2.1.2
Date: 2017-04-30
Author: Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
Email: jean-francois.martin(at)toulouse.inra.fr, melanie.petera(at)clermont.inra.fr, etienne.thevenot(at)cea.fr
Citation:
Licence: CeCILL
Reference history: W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12 and W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

Installation

• Configuration files:

  • batch_correction.xml (for the “Batch Correction” module)
  • determine_bc.xml (for the “Determine Batch Correction” module)
    

• Image files:

  • static/images/batch_correction.png
    
  • static/images/determine_batch_correction.png
    
  • static/images/pdf_plotsituation.png
    
  • static/images/Vdk_pdf1.png
    
  • static/images/Vdk_pdf2.png
    

• Wrapper files:

  • batch_correction_wrapper.R
    
  • batch_correction_all_loess_wrapper.R
    

• Script files:

  • Normalisation_QCpool.r
    
  • batch_correction_all_loess_script.R
    

• R packages

• batch from CRAN
  

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

• ade4 from CRAN
  

  all.packages("ade4", dep=TRUE)  
  

• pcaMethods from Bioconductor
  

  ce("http://www.bioconductor.org/biocLite.R")  
  Lite("pcaMethods")      
  

• ropls from Bioconductor
  

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

Tests

The code in the batch_correction_wrapper can be tested by running the runit/batchcorrection_runtests.R R file

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

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

Working example

See the reference histories W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12 and W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12

News

CHANGES IN VERSION 2.1.2

INTERNAL MODIFICATIONS

• Minor modifications in config file
  

CHANGES IN VERSION 2.1.0

INTERNAL MODIFICATIONS

• For PCA figure display only (“all_loess_” options): missing values are set to the minimum value before PCA computation is performed (with svd)

• Additional running and installation tests added with planemo, conda, and travis
  

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