Last data update: 2014.03.03
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msmsTests
Package: msmsTests
Type: Package
Title: LC-MS/MS Differential Expression Tests
Version: 1.10.0
Date: 2013-10-02
Author: Josep Gregori, Alex Sanchez, and Josep Villanueva
Maintainer: Josep Gregori i Font <josep.gregori@gmail.com>
Depends: R (>= 3.0.1), MSnbase, msmsEDA
Imports: edgeR, qvalue
Description: Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.
License: GPL-2
biocViews: Software, MassSpectrometry, Proteomics
NeedsCompilation: no
Packaged: 2016-05-04 05:02:35 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'msmsTests' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'msmsTests'
finding HTML links ... done
msms.edgeR html
finding level-2 HTML links ... done
msms.glm.pois html
msms.glm.qlll html
msms.spk html
msmsTests-package html
pval.by.fc html
res.volcanoplot html
test.results html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (msmsTests)
Making 'packages.html' ... done
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