bridge

Bayesian Robust Inference for Differential Gene Expression

Bioconductor version: Release (2.14)

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

Maintainer: Raphael Gottardo <raph at stat.ubc.ca>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("bridge")

To cite this package in a publication, start R and enter:

    citation("bridge")

Documentation

PDF R Script bridge Tutorial
PDF   Reference Manual

Details

biocViews DifferentialExpression, Microarray, OneChannel, Software, TwoChannel
Version 1.28.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License GPL (>= 2)
Depends R (>= 1.9.0), rama
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Package Downloads

Package Source bridge_1.28.0.tar.gz
Windows Binary bridge_1.28.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) bridge_1.28.0.tgz
Mac OS X 10.9 (Mavericks)
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