DOI: 10.18129/B9.bioc.msmsTests    

LC-MS/MS Differential Expression Tests

Bioconductor version: Release (3.6)

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>

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PDF R Script msmsTests: controlling batch effects by blocking
PDF R Script msmsTests: post test filters to improve reproducibility
PDF   Reference Manual


biocViews MassSpectrometry, Proteomics, Software
Version 1.16.0
In Bioconductor since BioC 2.13 (R-3.0) (4.5 years)
License GPL-2
Depends R (>= 3.0.1), MSnbase, msmsEDA
Imports edgeR, qvalue
Depends On Me
Imports Me
Suggests Me MSnID, RforProteomics
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