msmsTests: LC-MS/MS Differential Expression Tests
Version 1.14.0

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.

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AuthorJosep Gregori, Alex Sanchez, and Josep Villanueva
Bioconductor views MassSpectrometry Proteomics Software
Date of publicationNone
MaintainerJosep Gregori i Font <josep.gregori@gmail.com>
LicenseGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msmsTests")

Man pages

msms.edgeR: Spectral counts differential expression by edgeR
msms.glm.pois: Spectral counts differential expression by Poisson GLM
msms.glm.qlll: Spectral counts differential expression by quasi-likelihood...
msms.spk: Yeast lisate samples spiked with human proteins
msmsTests-package: LC-MS/MS Differential Expression Tests
pval.by.fc: Table of cumulative frequencies of p-values by log fold...
res.volcanoplot: Volcanoplot
test.results: Multitest p-value adjustment and post-test filter

Functions

glm.pois Source code
msms.edgeR Man page Source code
msms.glm.pois Man page Source code
msms.glm.qlll Man page Source code
msms.spk Man page
msmsTests Man page
msmsTests-package Man page
pval.by.fc Man page Source code
qp.test Source code
res.volcanoplot Man page Source code
test.results Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/msmsTest-functions.R
build
build/vignette.rds
data
data/msms.spk.rda
inst
inst/doc
inst/doc/msmsTests-Vignette.R
inst/doc/msmsTests-Vignette.Rnw
inst/doc/msmsTests-Vignette.pdf
inst/doc/msmsTests-Vignette2.R
inst/doc/msmsTests-Vignette2.Rnw
inst/doc/msmsTests-Vignette2.pdf
man
man/msms.edgeR.Rd
man/msms.glm.pois.Rd
man/msms.glm.qlll.Rd
man/msms.spk.Rd
man/msmsTests-package.Rd
man/pval.by.fc.Rd
man/res.volcanoplot.Rd
man/test.results.Rd
vignettes
vignettes/msmsTests-Vignette.Rnw
vignettes/msmsTests-Vignette2.Rnw
msmsTests documentation built on May 20, 2017, 10:31 p.m.