msmsTests: LC-MS/MS Differential Expression Tests

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msmsTests")
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
Version1.12.0

View on Bioconductor

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

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