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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/batch_correction).
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7
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8 ### Description
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9
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10 **Version:** 3.0.0
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11 **Date:** 2020-10-02
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12 **Author:** Jean-Francois Martin (INRAE, AXIOM), Melanie Petera (INRAE, PFEM), Marion Landi (PFEM), Franck Giacomoni (INRAE, PFEM), and Etienne A. Thevenot (CEA, LIST)
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13 **Email:** [jean-francois.martin(at)inrae.fr](mailto:jean-francois.martin@inrae.fr), [melanie.petera(at)inrae.fr](mailto:melanie.petera@inrae.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 * Wrapper files:
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28 + `batch_correction_3Lwrapper.R`
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29 + `batch_correction_all_loess_wrapper.R`
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30 * Script files:
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31 + `batch_correction_3Lfct.R`
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32 + `batch_correction_3Llauncher.R`
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33 + `batch_correction_all_loess_script.R`
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34 * R packages
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35 + **batch** from CRAN
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36
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37 ```r
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38 install.packages("batch", dep=TRUE)
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39 ```
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40
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41 + **ade4** from CRAN
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42
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43 ```r
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44 install.packages("ade4", dep=TRUE)
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45 ```
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46
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47 + **pcaMethods** from Bioconductor
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48
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49 ```r
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50 source("http://www.bioconductor.org/biocLite.R")
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51 biocLite("pcaMethods")
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52 ```
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53
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54 + **ropls** from Bioconductor
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55
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56 ```r
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57 source("http://www.bioconductor.org/biocLite.R")
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58 biocLite("ropls")
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59 ```
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60
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61 ### Tests
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62
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63 Some functional tests are provided in Galaxy format (see XML wrapper and test-data folder).
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64
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65 WIP: The code in the batch_correction_wrapper can be tested by running the `test/batchcorrection_runtests.R` R file
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66 You will need to install **RUnit** package in order to make it run:
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67 ```r
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68 install.packages('RUnit', dependencies = TRUE)
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69 ```
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70
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71 ### Working example
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72
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73 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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74
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75
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76 ### News
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77
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78 ###### CHANGES IN VERSION 3.0.0
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79
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80 NEW FEATURES
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81
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82 * Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata are now available in a dedicated parameter section
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83 * Addition of a sum of ions before/after plot for linear/lowess/loess methods
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84 * Addition of a third option in "Null values" parameter (renamed "unconsistant values") in linear/lowess/loess methods
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85 * linear/lowess/loess methods now handle NA in intensities and allow "blank" samples in the dataset
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86
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87 INTERNAL MODIFICATIONS
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88
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89 * XML optimisation using macros
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90 * Output name changes
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91 * linear/lowess/loess methods: disabling of RData output
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92 * linear/lowess/loess methods: split of tool-linked code and script-linked one
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93 * linear/lowess/loess methods: adjustments in the normalisation process to match matters linked to NA acceptance
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94 * linear/lowess/loess methods: better handling of special characters in IDs and column names
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95
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96 ###### CHANGES IN VERSION 2.2.4
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97
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98 INTERNAL MODIFICATIONS
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99
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100 Fixed bug for pool selection ("all_loess" methods)
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101
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102 ###### CHANGES IN VERSION 2.2.2
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103
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104 INTERNAL MODIFICATIONS
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105
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106 Fixed bug for color plot ("all_loess" methods)
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107
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108 ###### CHANGES IN VERSION 2.2.0
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109
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110 NEW FEATURE
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111
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112 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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113
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114 ##### CHANGES IN VERSION 2.1.2
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115
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116 INTERNAL MODIFICATIONS
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117
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118 * Minor modifications in config file
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119
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120 ##### CHANGES IN VERSION 2.1.0
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121
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122 INTERNAL MODIFICATIONS
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123
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124 * 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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125
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126 * Additional running and installation tests added with planemo, conda, and travis
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127
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128 * 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)
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