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XDE (version 2.18.0)
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
Description
Multi-level model for cross-study detection of differential gene expression.
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2.18.0
2.16.0
2.14.0
2.12.0
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Version
2.18.0
License
LGPL-2
Maintainer
Robert Scharpf
Last Published
May 10th, 2011
Functions in XDE (2.18.0)
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ExpressionSetList-class
A class for containing a list of ExpressionSets
xmcmc
Object of class XdeMcmc
output
Options for storing results of the MCMC chains
empiricalStart
Empirical starting values for the MCMC
tuning
Tuning parameters for Metropolis-Hastings proposals
Parameters-class
Container for XDE parameters
XdeMcmc-class
Class for storing output from the Bayesian model
posteriorAvg
Accessor and replacement methods for posterior averages of differential expression
pairs-methods
pairs function for high-throughput data
updates
Frequency of updating a parameter per MCMC iteration
symbolsInteresting
Useful for changing the look of pairs plots to emphasize concordant or discordant genes
ExpressionSetList-methods
Methods for ExpressionSetList
studyCenter
Center the expression values in a study to zero
iterations
Number of MCMC iterations
geneCenter
Center the expression values for each gene in a study to zero
thin
How often to write MCMC iterations to file
standardizeSamples
Centers the genes at zero and standardizes the samples to have variance 1
firstMcmc
Values for the first MCMC iteration
calculatePosteriorAvg
Calculate the posterior average for indicators of concordant and discordant differential expression
burnin
Indicator for running a MCMC burnin
xde
Fit the Bayesian hierarchical model for cross-study differential gene expression
ssStatistic
Calculate single study estimates of effect size
xsScores
Alternative cross-study scores of differential expression
expressionSetList
Example of ExpressionSetList
seed
Seed for the MCMC
hyperparameters
Accessor for hyperparameters of the Bayesian model
lastMcmc
MCMC values for the last iteration
XdeParameter-class
Container class for storing options of the Bayesian hierarchical model
zeroNu
Option for not modeling Nu