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1 Signal drift and batch-effect correction
2 ========================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batch_correction.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batch_correction).
7
8 ### Description
9
10 **Version:** 3.0.0
11 **Date:** 2020-10-02
12 **Author:** Jean-Francois Martin (INRAE, AXIOM), Melanie Petera (INRAE, PFEM), Marion Landi (PFEM), Franck Giacomoni (INRAE, PFEM), and Etienne A. Thevenot (CEA, LIST)
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)
14 **Citation:**
15 **Licence:** CeCILL
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)
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)
18
19 ### Installation
20
21 * Configuration files:
22 + `batch_correction.xml` (for the "Batch Correction" module)
23 + `determine_bc.xml` (for the "Determine Batch Correction" module)
24 * Image files:
25 + `static/images/batch_correction.png`
26 + `static/images/determine_batch_correction.png`
27 * Wrapper files:
28 + `batch_correction_3Lwrapper.R`
29 + `batch_correction_all_loess_wrapper.R`
30 * Script files:
31 + `batch_correction_3Lfct.R`
32 + `batch_correction_3Llauncher.R`
33 + `batch_correction_all_loess_script.R`
34 * R packages
35 + **batch** from CRAN
36
37 ```r
38 install.packages("batch", dep=TRUE)
39 ```
40
41 + **ade4** from CRAN
42
43 ```r
44 install.packages("ade4", dep=TRUE)
45 ```
46
47 + **pcaMethods** from Bioconductor
48
49 ```r
50 source("http://www.bioconductor.org/biocLite.R")
51 biocLite("pcaMethods")
52 ```
53
54 + **ropls** from Bioconductor
55
56 ```r
57 source("http://www.bioconductor.org/biocLite.R")
58 biocLite("ropls")
59 ```
60
61 ### Tests
62
63 Some functional tests are provided in Galaxy format (see XML wrapper and test-data folder).
64
65 WIP: The code in the batch_correction_wrapper can be tested by running the `test/batchcorrection_runtests.R` R file
66 You will need to install **RUnit** package in order to make it run:
67 ```r
68 install.packages('RUnit', dependencies = TRUE)
69 ```
70
71 ### Working example
72
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)
74
75
76 ### News
77
78 ###### CHANGES IN VERSION 3.0.0
79
80 NEW FEATURES
81
82 * Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata are now available in a dedicated parameter section
83 * Addition of a sum of ions before/after plot for linear/lowess/loess methods
84 * Addition of a third option in "Null values" parameter (renamed "unconsistant values") in linear/lowess/loess methods
85 * linear/lowess/loess methods now handle NA in intensities and allow "blank" samples in the dataset
86
87 INTERNAL MODIFICATIONS
88
89 * XML optimisation using macros
90 * Output name changes
91 * linear/lowess/loess methods: disabling of RData output
92 * linear/lowess/loess methods: split of tool-linked code and script-linked one
93 * linear/lowess/loess methods: adjustments in the normalisation process to match matters linked to NA acceptance
94 * linear/lowess/loess methods: better handling of special characters in IDs and column names
95
96 ###### CHANGES IN VERSION 2.2.4
97
98 INTERNAL MODIFICATIONS
99
100 Fixed bug for pool selection ("all_loess" methods)
101
102 ###### CHANGES IN VERSION 2.2.2
103
104 INTERNAL MODIFICATIONS
105
106 Fixed bug for color plot ("all_loess" methods)
107
108 ###### CHANGES IN VERSION 2.2.0
109
110 NEW FEATURE
111
112 Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata can be selected by the user (for compatibility with the MTBLS downloader)
113
114 ##### CHANGES IN VERSION 2.1.2
115
116 INTERNAL MODIFICATIONS
117
118 * Minor modifications in config file
119
120 ##### CHANGES IN VERSION 2.1.0
121
122 INTERNAL MODIFICATIONS
123
124 * For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd)
125
126 * Additional running and installation tests added with planemo, conda, and travis
127
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)