To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("msmsTests")

In most cases, you don't need to download the package archive at all.

msmsTests

 

LC-MS/MS Differential Expression Tests

Bioconductor version: Release (3.1)

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.

Author: Josep Gregori, Alex Sanchez, and Josep Villanueva

Maintainer: Josep Gregori i Font <josep.gregori at gmail.com>

Citation (from within R, enter citation("msmsTests")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("msmsTests")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("msmsTests")

 

PDF R Script msmsTests: controlling batch effects by blocking
PDF R Script msmsTests: post test filters to improve reproducibility
PDF   Reference Manual

Details

biocViews MassSpectrometry, Proteomics, Software
Version 1.6.0
In Bioconductor since BioC 2.13 (R-3.0) (2 years)
License GPL-2
Depends R (>= 3.0.1), MSnbase, msmsEDA
Imports edgeR, qvalue
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me MSnID, RforProteomics
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source msmsTests_1.6.0.tar.gz
Windows Binary msmsTests_1.6.0.zip
Mac OS X 10.6 (Snow Leopard) msmsTests_1.6.0.tgz
Mac OS X 10.9 (Mavericks) msmsTests_1.6.0.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/msmsTests/tree/release-3.1
Package Short Url http://bioconductor.org/packages/msmsTests/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center