bridge: Bayesian Robust Inference for Differential Gene Expression

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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.

Author
Raphael Gottardo
Date of publication
None
Maintainer
Raphael Gottardo <raph@stat.ubc.ca>
License
GPL (>= 2)
Version
1.38.0

View on Bioconductor

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...

Files in this package

bridge/DESCRIPTION
bridge/NAMESPACE
bridge/R
bridge/R/bridge.2samples.R
bridge/R/bridge.3samples.R
bridge/R/zzz.R
bridge/build
bridge/build/vignette.rds
bridge/data
bridge/data/hiv.rda
bridge/inst
bridge/inst/doc
bridge/inst/doc/bridge.R
bridge/inst/doc/bridge.Rnw
bridge/inst/doc/bridge.pdf
bridge/man
bridge/man/bridge.2samples.Rd
bridge/man/bridge.3samples.Rd
bridge/man/hiv.Rd
bridge/src
bridge/src/bridge2.affy.c
bridge/src/bridge2.c
bridge/src/bridge2_util.c
bridge/src/bridge2_util.h
bridge/src/bridge3.c
bridge/vignettes
bridge/vignettes/bridge.Rnw
bridge/vignettes/chicago.bst
bridge/vignettes/chicago.sty
bridge/vignettes/robust-testing.bib