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Last data update: 2014.03.03

R: Empirical starting values for the MCMC

empiricalStart

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(XDE)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XDE/empiricalStart.Rd_%03d_medium.png", width=480, height=480)
> ### Name: empiricalStart
> ### Title: Empirical starting values for the MCMC
> ### Aliases: empiricalStart
> ### Keywords: methods
> 
> ### ** Examples
> 
> library(XDE)
> data(expressionSetList)
> eList <- studyCenter(expressionSetList)
> empirical <- empiricalStart(eList, phenotypeLabel="adenoVsquamous", T_THRESH=3)
Loading required package: genefilter
> ##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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>