msmsTests

DOI: 10.18129/B9.bioc.msmsTests    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see msmsTests.

LC-MS/MS Differential Expression Tests

Bioconductor version: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("msmsTests")

For older versions of R, please refer to the appropriate Bioconductor release.

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 ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 1.22.0
In Bioconductor since BioC 2.13 (R-3.0) (6 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
Links To Me
Build Report  

Package Archives

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

Source Package msmsTests_1.22.0.tar.gz
Windows Binary msmsTests_1.22.0.zip
Mac OS X 10.11 (El Capitan) msmsTests_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msmsTests
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msmsTests
Package Short Url https://bioconductor.org/packages/msmsTests/
Package Downloads Report Download Stats

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