bridge: Bayesian Robust Inference for Differential Gene Expression
Version 1.40.0

Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.

Browse man pages Browse package API and functions Browse package files

AuthorRaphael Gottardo
Bioconductor views DifferentialExpression Microarray OneChannel TwoChannel
Date of publicationNone
MaintainerRaphael Gottardo <raph@stat.ubc.ca>
LicenseGPL (>= 2)
Version1.40.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bridge")

Man pages

bridge.2samples: Bayesian Robust Inference for Differential Gene Expression...
bridge.3samples: Bayesian Robust Inference for Differential Gene Expression...
hiv: Cellular gene expression upon human immunodeficiency virus...

Functions

bridge.2samples Man page
bridge.3samples Man page
hiv Man page
onLoad Source code

Files

DESCRIPTION
NAMESPACE
R
R/bridge.2samples.R
R/bridge.3samples.R
R/zzz.R
build
build/vignette.rds
data
data/hiv.rda
inst
inst/doc
inst/doc/bridge.R
inst/doc/bridge.Rnw
inst/doc/bridge.pdf
man
man/bridge.2samples.Rd
man/bridge.3samples.Rd
man/hiv.Rd
src
src/bridge2.affy.c
src/bridge2.c
src/bridge2_util.c
src/bridge2_util.h
src/bridge3.c
vignettes
vignettes/bridge.Rnw
vignettes/chicago.bst
vignettes/chicago.sty
vignettes/robust-testing.bib
bridge documentation built on May 20, 2017, 9:31 p.m.