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.

Author
Josep Gregori, Alex Sanchez, and Josep Villanueva
Date of publication
None
Maintainer
Josep Gregori i Font <josep.gregori@gmail.com>
License
GPL-2
Version
1.12.0

View on Bioconductor

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

Files in this package

msmsTests/DESCRIPTION
msmsTests/NAMESPACE
msmsTests/R
msmsTests/R/msmsTest-functions.R
msmsTests/build
msmsTests/build/vignette.rds
msmsTests/data
msmsTests/data/msms.spk.rda
msmsTests/inst
msmsTests/inst/doc
msmsTests/inst/doc/msmsTests-Vignette.R
msmsTests/inst/doc/msmsTests-Vignette.Rnw
msmsTests/inst/doc/msmsTests-Vignette.pdf
msmsTests/inst/doc/msmsTests-Vignette2.R
msmsTests/inst/doc/msmsTests-Vignette2.Rnw
msmsTests/inst/doc/msmsTests-Vignette2.pdf
msmsTests/man
msmsTests/man/msms.edgeR.Rd
msmsTests/man/msms.glm.pois.Rd
msmsTests/man/msms.glm.qlll.Rd
msmsTests/man/msms.spk.Rd
msmsTests/man/msmsTests-package.Rd
msmsTests/man/pval.by.fc.Rd
msmsTests/man/res.volcanoplot.Rd
msmsTests/man/test.results.Rd
msmsTests/vignettes
msmsTests/vignettes/msmsTests-Vignette.Rnw
msmsTests/vignettes/msmsTests-Vignette2.Rnw