xde {XDE}R Documentation

Fit the Bayesian hierarchical model for cross-study differential gene expression

Description

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

Usage

  
  xde(paramsMcmc, esetList, outputMcmc, batchSize=NULL, NCONC=2)

Arguments

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.

Details

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.

Value

Object of class XdeMcmc

Note

See the vignettes for XdeParameterClass and XDE.

Author(s)

R. Scharpf

References

R. Scharpf et al., A Bayesian Model for Cross-Study Differential Gene Expression, Technical Report 158, Johns Hopkins University, Department of Biostatistics, 2007

See Also

XdeMcmc-class, XdeParameter-class, ExpressionSetList-class

Examples

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

[Package XDE version 1.4.0 Index]