Mercurial > repos > melpetera > batchcorrection
comparison batchcorrection-57edfd3943ab/README.md @ 3:73892ef177e3 draft
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author | melpetera |
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date | Tue, 02 May 2017 09:47:22 -0400 |
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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/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection). | |
7 | |
8 ### Description | |
9 | |
10 **Version:** 2.1.2 | |
11 **Date:** 2017-04-30 | |
12 **Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) | |
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) | |
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 + `static/images/pdf_plotsituation.png` | |
28 + `static/images/Vdk_pdf1.png` | |
29 + `static/images/Vdk_pdf2.png` | |
30 * Wrapper files: | |
31 + `batch_correction_wrapper.R` | |
32 + `batch_correction_all_loess_wrapper.R` | |
33 * Script files: | |
34 + `Normalisation_QCpool.r` | |
35 + `batch_correction_all_loess_script.R` | |
36 * R packages | |
37 + **batch** from CRAN | |
38 | |
39 ```r | |
40 install.packages("batch", dep=TRUE) | |
41 ``` | |
42 | |
43 + **ade4** from CRAN | |
44 | |
45 ```r | |
46 install.packages("ade4", dep=TRUE) | |
47 ``` | |
48 | |
49 + **pcaMethods** from Bioconductor | |
50 | |
51 ```r | |
52 source("http://www.bioconductor.org/biocLite.R") | |
53 biocLite("pcaMethods") | |
54 ``` | |
55 | |
56 + **ropls** from Bioconductor | |
57 | |
58 ```r | |
59 source("http://www.bioconductor.org/biocLite.R") | |
60 biocLite("ropls") | |
61 ``` | |
62 | |
63 ### Tests | |
64 | |
65 The code in the batch_correction_wrapper can be tested by running the `runit/batchcorrection_runtests.R` R file | |
66 | |
67 You will need to install **RUnit** package in order to make it run: | |
68 ```r | |
69 install.packages('RUnit', dependencies = TRUE) | |
70 ``` | |
71 | |
72 ### Working example | |
73 | |
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) | |
75 | |
76 | |
77 ### News | |
78 | |
79 ##### CHANGES IN VERSION 2.1.2 | |
80 | |
81 INTERNAL MODIFICATIONS | |
82 | |
83 * Minor modifications in config file | |
84 | |
85 ##### CHANGES IN VERSION 2.1.0 | |
86 | |
87 INTERNAL MODIFICATIONS | |
88 | |
89 * For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd) | |
90 | |
91 * Additional running and installation tests added with planemo, conda, and travis | |
92 | |
93 * 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) |