$	XdeMcmc-class
$,Parameters-method	Parameters-class
$,XdeMcmc-method	XdeMcmc-class
$<-,Parameters-method	Parameters-class
.standardizedDelta,XdeMcmc-method	XdeMcmc-class
bayesianEffectSize	XdeMcmc-class
bayesianEffectSize,XdeMcmc-method	XdeMcmc-class
bayesianEffectSize<-	XdeMcmc-class
bayesianEffectSize<-,XdeMcmc,matrix-method	XdeMcmc-class
burnin	burnin
burnin,XdeParameter-method	XdeParameter-class
burnin<-	burnin
burnin<-,XdeParameter,logical-method	XdeParameter-class
calculateBayesianEffectSize	XdeMcmc-class
calculateBayesianEffectSize,XdeMcmc-method	XdeMcmc-class
calculatePosteriorAvg	calculatePosteriorAvg
calculatePosteriorAvg,XdeMcmc-method	XdeMcmc-class
coerce,list,ExpressionSetList-method	ExpressionSetList-class
coerce,XdeParameter,Parameters-method	Parameters-class
coerce,XdeParameter,Params-method	XdeParameter-class
dim,ExpressionSetList-method	ExpressionSetList-class
directory	XdeMcmc-class
directory,XdeMcmc-method	XdeMcmc-class
directory,XdeParameter-method	XdeParameter-class
directory<-	XdeParameter-class
directory<-,XdeParameter-method	XdeParameter-class
empiricalStart	empiricalStart
expressionSetList	expressionSetList
ExpressionSetList-class	ExpressionSetList-class
ExpressionSetList-methods	ExpressionSetList-methods
featureNames,ExpressionSetList-method	ExpressionSetList-class
featureNames,XdeMcmc-method	XdeMcmc-class
firstMcmc	firstMcmc
firstMcmc,XdeParameter-method	XdeParameter-class
firstMcmc<-	firstMcmc
firstMcmc<-,XdeParameter,environment-method	XdeParameter-class
firstMcmc<-,XdeParameter,list-method	XdeParameter-class
geneCenter	geneCenter
geneCenter,ExpressionSetList-method	ExpressionSetList-class
hyperparameters	hyperparameters
hyperparameters,XdeParameter-method	XdeParameter-class
hyperparameters<-	hyperparameters
hyperparameters<-,XdeParameter-method	XdeParameter-class
initialize,XdeMcmc-method	XdeMcmc-class
initialize,XdeParameter-method	XdeParameter-class
iterations	iterations
iterations,XdeMcmc-method	XdeMcmc-class
iterations,XdeParameter-method	XdeParameter-class
iterations<-	iterations
iterations<-,XdeParameter,integer-method	XdeParameter-class
iterations<-,XdeParameter,numeric-method	XdeParameter-class
lapply,ExpressionSetList-method	ExpressionSetList-class
lastMcmc	lastMcmc
lastMcmc,XdeMcmc-method	XdeMcmc-class
lastMcmc<-	lastMcmc
nrow,ExpressionSetList-method	ExpressionSetList-class
nrow,XdeMcmc-method	XdeMcmc-class
nSamples	ExpressionSetList-class
nSamples,ExpressionSetList-method	ExpressionSetList-class
output	output
output,XdeMcmc-method	XdeMcmc-class
output,XdeParameter-method	XdeParameter-class
output<-	output
output<-,XdeParameter-method	XdeParameter-class
pairs,data.frame-method	pairs
pairs,matrix-method	pairs
pairs-methods	pairs
Parameters-class	Parameters-class
pca,ExpressionSetList-method	ExpressionSetList-class
pData,ExpressionSetList-method	ExpressionSetList-class
phenotype	ExpressionSetList-methods
phenotype,ExpressionSetList,character-method	ExpressionSetList-class
phenotypeLabel	XdeParameter-class
phenotypeLabel,XdeParameter-method	XdeParameter-class
phenotypeLabel<-	XdeParameter-class
phenotypeLabel<-,XdeParameter,character-method	XdeParameter-class
plot,XdeMcmc,ANY-method	XdeMcmc-class
plot,XdeMcmc-method	XdeMcmc-class
posteriorAvg	posteriorAvg
posteriorAvg,XdeMcmc-method	XdeMcmc-class
posteriorAvg<-	posteriorAvg
posteriorAvg<-,XdeMcmc,matrix-method	XdeMcmc-class
savedIterations	XdeParameter-class
savedIterations,XdeParameter-method	XdeParameter-class
seed	seed
seed,XdeMcmc-method	XdeMcmc-class
seed,XdeParameter-method	XdeParameter-class
seed<-	seed
seed<-,XdeParameter,integer-method	XdeParameter-class
seed<-,XdeParameter,numeric-method	XdeParameter-class
show,Parameters-method	Parameters-class
show,XdeMcmc-method	XdeMcmc-class
show,XdeParameter-method	XdeParameter-class
showIterations	XdeParameter-class
showIterations,XdeParameter-method	XdeParameter-class
showIterations<-	XdeParameter-class
showIterations<-,XdeParameter-method	XdeParameter-class
ssStatistic	ssStatistic
standardizeSamples	standardizeSamples
standardizeSamples,ExpressionSetList-method	ExpressionSetList-class
studyCenter	studyCenter
studyCenter,ExpressionSetList-method	ExpressionSetList-class
studyNames	XdeParameter-class
studyNames,XdeMcmc-method	XdeMcmc-class
studyNames,XdeParameter-method	XdeParameter-class
studyNames<-	XdeParameter-class
studyNames<-,XdeParameter-method	XdeParameter-class
symbolsInteresting	symbolsInteresting
thin	thin
thin,XdeParameter-method	XdeParameter-class
thin<-	thin
thin<-,XdeParameter,numeric-method	XdeParameter-class
tuning	tuning
tuning,XdeParameter-method	XdeParameter-class
tuning<-	tuning
tuning<-,XdeParameter-method	XdeParameter-class
updates	updates
updates,XdeParameter-method	XdeParameter-class
updates<-	updates
updates<-,XdeParameter-method	XdeParameter-class
xde	xde
XdeMcmc-class	XdeMcmc-class
XdeParameter-class	XdeParameter-class
xmcmc	xmcmc
xsScores	xsScores
zeroNu	zeroNu
zeroNu,ExpressionSetList-method	ExpressionSetList-class
[,ExpressionSetList,ANY,ANY,ANY-method	ExpressionSetList-methods
[,ExpressionSetList-method	ExpressionSetList-class
[[,Parameters-method	Parameters-class
[[<-,Parameters-method	Parameters-class
