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