empiricalStart: Empirical starting values for the MCMC

In XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Description

Empirical starting values for the MCMC are based on data in objects of class ExpressionSetList

Usage

empiricalStart(object, zeroNu = FALSE, phenotypeLabel, one.delta=FALSE, T_THRESH=4)

Arguments

object	An object of class ExpressionSetList
zeroNu	Logical: if TRUE, the nu in the Bayesian model are not modeled – set to zero and not updated in the MCMC. Setting zeroNu to TRUE should be regarded as experimental
phenotypeLabel	character: binary phenotype. phenotypeLabel must be in the varLabels of each ExpressionSet object
one.delta	delta in the Bayesian model is a gene-specific indicator for differential expression. If one.delta is FALSE, we assume that a gene can be differentially expressed in a subset of studies. When TRUE, we assume that a gene is differentially expressed in all studies or in none.
T_THRESH	A threshold of t-statistics (calculated row-wise for each study) for determining starting values of the differential expression indicator, delta.

Value

A list containing starting values for the MCMC that are derived from empirical estimates of the data.

Author(s)

R. Scharpf

See Also

zeroNu, XdeParameter-class, ExpressionSetList-class

Examples

library(XDE)
data(expressionSetList)
eList <- studyCenter(expressionSetList)
empirical <- empiricalStart(eList, phenotypeLabel="adenoVsquamous", T_THRESH=3)
##By default, initial values for the MCMC are sampled from the prior
##when initializing an object of class XdeParamater
params <- new("XdeParameter", esetList=eList,
	      phenotypeLabel="adenoVsquamous", one.delta=FALSE, burnin=TRUE)
##The initial values can be replaced by empirical values as follows:
firstMcmc(params) <- empirical

XDE documentation built on Nov. 8, 2020, 5:02 p.m.