$	XdeMcmc-class
$,Parameters-method	Parameters-class
$,XdeMcmc-method	XdeMcmc-class
$<-,Parameters-method	Parameters-class
.integrativeCorrelationFilter,ExpressionSetList-method	ExpressionSetList-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
rupdateAlpha_MRF	RUpdates
rupdateANu	RUpdates
rupdateBDDelta	RUpdates
rupdateBetag_MRF	RUpdates
rupdateBeta_MRF	RUpdates
rupdateC2	RUpdates
rupdateC2DDelta	RUpdates
rupdateDDelta	RUpdates
rupdateDeltaDDelta	RUpdates
rupdateDeltaDDelta_MRF	RUpdates
rupdateGamma2	RUpdates
rupdateGamma2Nu	RUpdates
rupdateL	RUpdates
rupdateLambda	RUpdates
rupdateLambdaPhi	RUpdates
rupdateLSigma2	RUpdates
rupdateNu	RUpdates
rupdatePhi	RUpdates
rupdateRC2	RUpdates
rupdateRDDelta	RUpdates
rupdateRhoGamma2	RUpdates
rupdateRhoNu	RUpdates
rupdateSigma2	RUpdates
rupdateT	RUpdates
rupdateTau2RDDelta	RUpdates
rupdateTau2RhoNu	RUpdates
rupdateTheta	RUpdates
rupdateThetaPhi	RUpdates
rupdateTSigma2	RUpdates
rupdateXi	RUpdates
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-method	ExpressionSetList-class
[[,Parameters-method	Parameters-class
[[<-,Parameters-method	Parameters-class
