Mercurial > repos > ethevenot > batchcorrection

## Signal drift and batch-effect correction
#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project

Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection).

### Description

**Version:** 2.0.6
**Date:** 2016-08-02
**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](mailto:jean-francois.martin@toulouse.inra.frr), [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
**Citation:**
**Licence:** CeCILL
**Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published)
**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) 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**
    + **miniTools.R**
    + **RcheckLibrary.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

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

### News

##### CHANGES IN VERSION 2.0.6

INTERNAL MODIFICATIONS

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

##### CHANGES IN VERSION 2.0.4

INTERNAL MODIFICATION

    o 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)

***
author	ethevenot
date	Thu, 04 Aug 2016 11:40:35 -0400
parents
children