Entry: ExpressionSetList-class
Aliases: ExpressionSetList-class .integrativeCorrelationFilter,ExpressionSetList-method [,ExpressionSetList-method coerce,list,ExpressionSetList-method dim,ExpressionSetList-method featureNames,ExpressionSetList-method geneCenter,ExpressionSetList-method lapply,ExpressionSetList-method nSamples nSamples,ExpressionSetList-method nrow,ExpressionSetList-method pData,ExpressionSetList-method pca,ExpressionSetList-method standardizeSamples,ExpressionSetList-method studyCenter,ExpressionSetList-method zeroNu,ExpressionSetList-method
Keywords: classes
Description: A class for containing a list of ExpressionSets
URL: ../../../library/XDE/html/ExpressionSetList-class.html

Entry: XdeMcmc-class
Aliases: XdeMcmc-class $ $,XdeMcmc-method .standardizedDelta,XdeMcmc-method bayesianEffectSize bayesianEffectSize,XdeMcmc-method bayesianEffectSize<- bayesianEffectSize<-,XdeMcmc,matrix-method calculateBayesianEffectSize calculateBayesianEffectSize,XdeMcmc-method calculatePosteriorAvg,XdeMcmc-method directory directory,XdeMcmc-method featureNames,XdeMcmc-method initialize,XdeMcmc-method iterations,XdeMcmc-method lastMcmc,XdeMcmc-method nrow,XdeMcmc-method output,XdeMcmc-method plot,XdeMcmc-method plot,XdeMcmc,ANY-method posteriorAvg,XdeMcmc-method posteriorAvg<-,XdeMcmc,matrix-method seed,XdeMcmc-method show,XdeMcmc-method studyNames,XdeMcmc-method
Keywords: classes
Description: Class for storing output from the Bayesian model
URL: ../../../library/XDE/html/XdeMcmc-class.html

Entry: XdeParameter-class
Aliases: XdeParameter-class burnin,XdeParameter-method burnin<-,XdeParameter,logical-method directory,XdeParameter-method directory<- directory<-,XdeParameter-method firstMcmc,XdeParameter-method firstMcmc<-,XdeParameter,environment-method firstMcmc<-,XdeParameter,list-method hyperparameters,XdeParameter-method hyperparameters<-,XdeParameter-method initialize,XdeParameter-method iterations,XdeParameter-method iterations<-,XdeParameter,numeric-method iterations<-,XdeParameter,integer-method output,XdeParameter-method output<-,XdeParameter-method phenotypeLabel phenotypeLabel<- phenotypeLabel,XdeParameter-method phenotypeLabel<-,XdeParameter,character-method savedIterations savedIterations,XdeParameter-method seed,XdeParameter-method seed<-,XdeParameter,integer-method seed<-,XdeParameter,numeric-method show,XdeParameter-method showIterations showIterations<- showIterations,XdeParameter-method showIterations<-,XdeParameter-method studyNames studyNames<- studyNames,XdeParameter-method studyNames<-,XdeParameter-method thin,XdeParameter-method thin<-,XdeParameter,numeric-method tuning,XdeParameter-method tuning<-,XdeParameter-method updates,XdeParameter-method updates<-,XdeParameter-method
Keywords: classes
Description: Container class for storing options of the Bayesian hierarchical model
URL: ../../../library/XDE/html/XdeParameter-class.html

Entry: burnin
Aliases: burnin burnin<-
Keywords: methods
Description: Indicator for running a MCMC burnin
URL: ../../../library/XDE/html/burnin.html

Entry: calculatePosteriorAvg
Aliases: calculatePosteriorAvg
Keywords: manip
Description: Calculate the posterior average for indicators of concordant and discordant differential expression
URL: ../../../library/XDE/html/calculatePosteriorAvg.html

Entry: empiricalStart
Aliases: empiricalStart
Keywords: methods
Description: Empirical starting values for the MCMC
URL: ../../../library/XDE/html/empiricalStart.html

Entry: expressionSetList
Aliases: expressionSetList
Keywords: datasets
Description: Example of ExpressionSetList
URL: ../../../library/XDE/html/expressionSetList.html

Entry: firstMcmc
Aliases: firstMcmc firstMcmc<-
Keywords: methods
Description: Values for the first MCMC iteration
URL: ../../../library/XDE/html/firstMcmc.html

Entry: geneCenter
Aliases: geneCenter
Keywords: methods
Description: Center the expression values for each gene in a study to zero
URL: ../../../library/XDE/html/geneCenter.html

Entry: hyperparameters
Aliases: hyperparameters hyperparameters<-
Keywords: methods
Description: Accessor for hyperparameters of the Bayesian model
URL: ../../../library/XDE/html/hyperparameters.html

Entry: iterations
Aliases: iterations iterations<-
Keywords: methods
Description: Number of MCMC iterations
URL: ../../../library/XDE/html/iterations.html

Entry: lastMcmc
Aliases: lastMcmc lastMcmc<-
Keywords: methods
Description: MCMC values for the last iteration
URL: ../../../library/XDE/html/lastMcmc.html

Entry: output
Aliases: output output<-
Keywords: methods
Description: Options for storing results of the MCMC chains
URL: ../../../library/XDE/html/output.html

Entry: pairs-methods
Aliases: pairs-methods pairs,matrix-method pairs,data.frame-method
Keywords: methods hplot
Description: pairs function for high-throughput data
URL: ../../../library/XDE/html/pairs.html

Entry: posteriorAvg
Aliases: posteriorAvg posteriorAvg<-
Keywords: methods
Description: Accessor and replacement methods for posterior averages of differential expression
URL: ../../../library/XDE/html/posteriorAvg.html

Entry: seed
Aliases: seed seed<-
Keywords: methods
Description: Seed for the MCMC
URL: ../../../library/XDE/html/seed.html

Entry: ssStatistic
Aliases: ssStatistic
Keywords: methods
Description: Calculate single study estimates of effect size
URL: ../../../library/XDE/html/ssStatistic.html

Entry: standardizeSamples
Aliases: standardizeSamples
Keywords: methods
Description: Centers the genes at zero and standardizes the samples to have variance 1
URL: ../../../library/XDE/html/standardizeSamples.html

Entry: studyCenter
Aliases: studyCenter
Keywords: methods
Description: Center the expression values in a study to zero
URL: ../../../library/XDE/html/studyCenter.html

Entry: symbolsInteresting
Aliases: symbolsInteresting
Keywords: dplot
Description: Useful for changing the look of pairs plots to emphasize concordant or discordant genes
URL: ../../../library/XDE/html/symbolsInteresting.html

Entry: thin
Aliases: thin thin<-
Keywords: methods
Description: How often to write MCMC iterations to file
URL: ../../../library/XDE/html/thin.html

Entry: tuning
Aliases: tuning tuning<-
Keywords: methods
Description: Tuning parameters for Metropolis-Hastings proposals
URL: ../../../library/XDE/html/tuning.html

Entry: updates
Aliases: updates updates<-
Keywords: methods
Description: Frequency of updating a parameter per MCMC iteration
URL: ../../../library/XDE/html/updates.html

Entry: xde
Aliases: xde
Keywords: models multivariate
Description: Fit the Bayesian hierarchical model for cross-study differential gene expression
URL: ../../../library/XDE/html/xde.html

Entry: xmcmc
Aliases: xmcmc
Keywords: datasets
Description: Object of class XdeMcmc
URL: ../../../library/XDE/html/xmcmc.html

Entry: xsScores
Aliases: xsScores
Keywords: htest models
Description: Alternative cross-study scores of differential expression
URL: ../../../library/XDE/html/xsScores.html

Entry: zeroNu
Aliases: zeroNu
Keywords: methods
Description: Option for not modeling Nu
URL: ../../../library/XDE/html/zeroNu.html
