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1 Signal drift and batch-effect correction
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2 ========================================
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3
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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5
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6 Status: [](https://travis-ci.org/workflow4metabolomics/batchcorrection).
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7
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8 ### Description
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9
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10 **Version:** 2.2.4
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11 **Date:** 2019-01-22
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12 **Author:** Jean-Francois Martin (INRA, AXIOM), Melanie Petera (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thevenot (CEA, LIST)
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13 **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)
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14 **Citation:**
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12)
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17 **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)
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18
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19 ### Installation
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20
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21 * Configuration files:
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22 + `batch_correction.xml` (for the "Batch Correction" module)
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23 + `determine_bc.xml` (for the "Determine Batch Correction" module)
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24 * Image files:
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25 + `static/images/batch_correction.png`
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26 + `static/images/determine_batch_correction.png`
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27 + `static/images/pdf_plotsituation.png`
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28 + `static/images/Vdk_pdf1.png`
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29 + `static/images/Vdk_pdf2.png`
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30 * Wrapper files:
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31 + `batch_correction_wrapper.R`
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32 + `batch_correction_all_loess_wrapper.R`
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33 * Script files:
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34 + `Normalisation_QCpool.r`
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35 + `batch_correction_all_loess_script.R`
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36 * R packages
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37 + **batch** from CRAN
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38
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39 ```r
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40 install.packages("batch", dep=TRUE)
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41 ```
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42
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43 + **ade4** from CRAN
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44
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45 ```r
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46 install.packages("ade4", dep=TRUE)
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47 ```
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48
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49 + **pcaMethods** from Bioconductor
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50
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51 ```r
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52 source("http://www.bioconductor.org/biocLite.R")
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53 biocLite("pcaMethods")
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54 ```
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55
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56 + **ropls** from Bioconductor
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57
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58 ```r
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59 source("http://www.bioconductor.org/biocLite.R")
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60 biocLite("ropls")
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61 ```
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62
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63 ### Tests
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64
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65 The code in the batch_correction_wrapper can be tested by running the `runit/batchcorrection_runtests.R` R file
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66
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67 You will need to install **RUnit** package in order to make it run:
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68 ```r
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69 install.packages('RUnit', dependencies = TRUE)
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70 ```
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71
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72 ### Working example
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73
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74 See the reference histories [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12)
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75
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76
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77 ### News
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78
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79 ###### CHANGES IN VERSION 2.2.4
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80
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81 INTERNAL MODIFICATIONS
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82
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83 Fixed bug for pool selection ("all_loess" methods)
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84
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85 ###### CHANGES IN VERSION 2.2.2
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86
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87 INTERNAL MODIFICATIONS
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88
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89 Fixed bug for color plot ("all_loess" methods)
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90
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91 ###### CHANGES IN VERSION 2.2.0
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92
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93 NEW FEATURE
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94
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95 Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata can be selected by the user (for compatibility with the MTBLS downloader)
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96
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97 ##### CHANGES IN VERSION 2.1.2
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98
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99 INTERNAL MODIFICATIONS
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100
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101 * Minor modifications in config file
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102
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103 ##### CHANGES IN VERSION 2.1.0
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104
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105 INTERNAL MODIFICATIONS
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106
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107 * For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd)
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108
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109 * Additional running and installation tests added with planemo, conda, and travis
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110
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111 * 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) |
