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 (2.14)

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 1.2.0
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2
Depends R (>= 3.0.1), MSnbase, msmsEDA
Imports edgeR, qvalue
Suggests
System Requirements
URL
Depends On Me
Imports Me
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Package Archives

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

Package Source msmsTests_1.2.0.tar.gz
Windows Binary msmsTests_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) msmsTests_1.2.0.tgz
Mac OS X 10.9 (Mavericks) msmsTests_1.2.0.tgz
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