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

msmsTests

LC-MS/MS Differential Expression Tests

Bioconductor version: 2.13

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>

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	1.0.0
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
Suggests Me

Package Archives

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

Package Source	msmsTests_1.0.0.tar.gz
Windows Binary	msmsTests_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	msmsTests_1.0.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats