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author ethevenot
date Sat, 06 Aug 2016 12:07:13 -0400
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1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA) 1 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)
2 ===================================================== 2 =====================================================
3 3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project 4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5 5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate). 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate).
7 7
8 ## Description 8 ### Description
9 9
10 **Version:** 2.3.4 10 **Version:** 2.3.6
11 **Date:** 2016-07-30 11 **Date:** 2016-08-05
12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) 12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) 13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
14 **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) 14 **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)
15 **Licence:** CeCILL 15 **Licence:** CeCILL
16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) 16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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) 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 18
19 ## Installation 19 ### Installation
20 20
21 * Configuration file: `multivariate_config.xml`. 21 * Configuration file: `multivariate_config.xml`
22 * Image files: 22 * Image files:
23 + `static/images/multivariate_workflowPositionImage.png`. 23 + `static/images/multivariate_workflowPositionImage.png`
24 + `static/images/multivariate_workingExampleImage.png`. 24 + `static/images/multivariate_workingExampleImage.png`
25 * Wrapper file: `multivariate_wrapper.R`. 25 * Wrapper file: `multivariate_wrapper.R`
26 * R packages 26 * R packages
27 + **batch** from CRAN 27 + **batch** from CRAN
28 28
29 ```r 29 ```r
30 install.packages("batch", dep=TRUE) 30 install.packages("batch", dep=TRUE)
35 ```r 35 ```r
36 source("http://www.bioconductor.org/biocLite.R") 36 source("http://www.bioconductor.org/biocLite.R")
37 biocLite("ropls") 37 biocLite("ropls")
38 ``` 38 ```
39 39
40 ## Tests 40 ### Tests
41 41
42 The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R. 42 The code in the wrapper can be tested by running the `runit/multivariate_runtests.R` R file
43 43
44 You will need to install **RUnit** package in order to make it run: 44 You will need to install **RUnit** package in order to make it run:
45 ```r 45 ```r
46 install.packages('RUnit', dependencies = TRUE) 46 install.packages('RUnit', dependencies = TRUE)
47 ``` 47 ```
48 48
49 ## News 49 ### Working example
50 50
51 ### CHANGES IN VERSION 2.3.4 51 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
52
53 ### News
54
55 ###### CHANGES IN VERSION 2.3.6
56
57 INTERNAL MODIFICATION
58
59 * minor internal modifications
60
61 ###### CHANGES IN VERSION 2.3.4
52 62
53 INTERNAL MODIFICATION 63 INTERNAL MODIFICATION
54 64
55 * minor update of .shed.yml 65 * minor update of .shed.yml
56
57 ***
58 66
59 ### CHANGES IN VERSION 2.3.2 67 ###### CHANGES IN VERSION 2.3.2
60 68
61 INTERNAL MODIFICATION 69 INTERNAL MODIFICATION
62 70
63 * Modification of the `multivariate_wrapper.R` file to handle **ropls** package versions of 1.3.15 and above (i.e. after switching to S4 classes). 71 * Modification of the `multivariate_wrapper.R` file to handle **ropls** package versions of 1.3.15 and above (i.e. after switching to S4 classes)
64
65 ***
66 72
67 ### CHANGES IN VERSION 2.3.0 73 ###### CHANGES IN VERSION 2.3.0
68 74
69 NEW FEATURES 75 NEW FEATURES
70 76
71 * **Predictions** now available (see the 'Samples to be tested' argument). 77 * **Predictions** now available (see the 'Samples to be tested' argument)
72 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section). 78 * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section)
73 * **Multiclass PLS-DA** implemented (see the 'comments' section). 79 * **Multiclass PLS-DA** implemented (see the 'comments' section)
74
75 ***