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

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Fits the Bayesian hierarchical model for cross-study differential gene expression.

1 2	xde(paramsMcmc, esetList, outputMcmc, batchSize=NULL, NCONC=2, center=TRUE, ...)

`paramsMcmc`	Object of class `XdeParameter`
`esetList`	Object of class `ExpressionSetList`
`outputMcmc`	Object of class `XdeMcmc` (optional)
`batchSize`	Integer or NULL. The number of iterations written to log files before summarizing the chain and then removing. Experimental.
`NCONC`	The number of studies for which a gene must be differentially expressed in the same direction to be considered as concordantly differentially expressed.
`center`	Logical. If TRUE, each study is centered to have mean zero.
`...`	Additional arguments passed to `xdeFit`.

Details for fitting the Bayesian model are discussed elsewhere (see citation below and XdeParameterClass vignette)

If an integer is specified for the batchSize, summary statistics for the log-files are calculated for every batchSize iterations. The log files are then removed and the next iteration will start a new log file. This allows one to do many iterations without creating enormous log files. This is only reasonable to do if one has already assessed convergence.

Object of class XdeMcmc

See the vignettes for XdeParameterClass and XDE.

R. Scharpf

R. Scharpf et al., A Bayesian Model for Cross-Study Differential Gene Expression, JASA 2009, p1295–1310.

XdeMcmc-class, XdeParameter-class, ExpressionSetList-class

## Not run: 
  data(expressionSetList)
  xparam <- new("XdeParameter", phenotypeLabel="adenoVsquamous", esetList=expressionSetList)
  iterations(xparam) <- 10
  fit <- xde(xparam, esetList=expressionSetList)

## End(Not run)