Mercurial > repos > melpetera > batchcorrection

Signal drift and batch-effect correction
========================================

A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure

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

### Description

**Version:** 2.0.8
**Date:** 2016-10-09
**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`
     + `batch_correction_all_loess_script.R`
* R packages
  + **batch** from CRAN

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

  + **ade4** from CRAN

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

 + **pcaMethods** from Bioconductor

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

 + **ropls** from Bioconductor

    ```r
    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` R file

You will need to install **RUnit** package in order to make it run:
```r
install.packages('RUnit', dependencies = TRUE)
```

### Working example

See also the reference history **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)

### News

##### CHANGES IN VERSION 2.0.8

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)

##### CHANGES IN VERSION 2.0.6

INTERNAL MODIFICATIONS

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

##### CHANGES IN VERSION 2.0.4

INTERNAL MODIFICATION

 * 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	melpetera
date	Sun, 09 Oct 2016 09:54:00 -0400
parents	71d83d8920bf
children