empiricalStart {XDE} | R Documentation

## Empirical starting values for the MCMC

### 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

[Package XDE version 2.28.0 Index]