msmsTests

DOI: 10.18129/B9.bioc.msmsTests    

LC-MS/MS Differential Expression Tests

Bioconductor version: Release (3.15)

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 "4.2") and enter:

if (!require("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 1.34.0
In Bioconductor since BioC 2.13 (R-3.0) (9 years)
License GPL-2
Depends R (>= 3.0.1), MSnbase, msmsEDA
Imports edgeR, qvalue
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Depends On Me
Imports Me MSnID
Suggests Me RforProteomics
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Build Report  

Package Archives

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

Source Package msmsTests_1.34.0.tar.gz
Windows Binary msmsTests_1.34.0.zip
macOS Binary (x86_64) msmsTests_1.34.0.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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