Signal drift and batch-effect correction

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 3.0.0
Date: 2020-10-02
Author: Jean-Francois Martin (INRAE, AXIOM), Melanie Petera (INRAE, PFEM), Marion Landi (PFEM), Franck Giacomoni (INRAE, PFEM), and Etienne A. Thevenot (CEA, LIST)
Email: jean-francois.martin(at)inrae.fr, melanie.petera(at)inrae.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
• Wrapper files:
  • batch_correction_3Lwrapper.R
  • batch_correction_all_loess_wrapper.R
• Script files:
  • batch_correction_3Lfct.R
  • batch_correction_3Llauncher.R
  • batch_correction_all_loess_script.R
• R packages

  • batch from CRAN

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

  • ade4 from CRAN

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

• pcaMethods from Bioconductor

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

• ropls from Bioconductor

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

Tests

Some functional tests are provided in Galaxy format (see XML wrapper and test-data folder).

WIP: The code in the batch_correction_wrapper can be tested by running the test/batchcorrection_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 reference histories W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12 and W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12

News

CHANGES IN VERSION 3.0.0

NEW FEATURES

• Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata are now available in a dedicated parameter section
• Addition of a sum of ions before/after plot for linear/lowess/loess methods
• Addition of a third option in "Null values" parameter (renamed "unconsistant values") in linear/lowess/loess methods
• linear/lowess/loess methods now handle NA in intensities and allow "blank" samples in the dataset

INTERNAL MODIFICATIONS

• XML optimisation using macros
• Output name changes
• linear/lowess/loess methods: disabling of RData output
• linear/lowess/loess methods: split of tool-linked code and script-linked one
• linear/lowess/loess methods: adjustments in the normalisation process to match matters linked to NA acceptance
• linear/lowess/loess methods: better handling of special characters in IDs and column names

CHANGES IN VERSION 2.2.4

INTERNAL MODIFICATIONS

Fixed bug for pool selection ("all_loess" methods)

CHANGES IN VERSION 2.2.2

INTERNAL MODIFICATIONS

Fixed bug for color plot ("all_loess" methods)

CHANGES IN VERSION 2.2.0

NEW FEATURE

Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata can be selected by the user (for compatibility with the MTBLS downloader)

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)