bgCorrectPara {affyPara}R Documentation

Parallelized Background Correction

Description

Parallelized functions for background correction of probe intensities.

Usage

bgCorrectPara(cluster,
        object, phenoData = new("AnnotatedDataFrame"), method, 
        verbose = FALSE)

bgCorrectParaSF(method) 

Arguments

cluster A cluster object obtained from the function makeCluster in the SNOW package.
object An object of class AffyBatch OR a character vector with the names of CEL files OR a (partitioned) list of character vectors with CEL file names.
phenoData An AnnotatedDataFrame object
method A character that defines what background correction method will be used. Available methods are given by bg.correct.methods. The name of the method to apply must be double-quoted.
verbose A logical value. If TRUE it writes out some messages.

Details

bgCorrectPara is the parallelized function for background correction of probe intensities. For serial function an more details see bg.correct.

For using this function a computer cluster using the snow package has to be started.

bgCorrectParaSF is a internal function which will be executed at slaves.

bgCorrectParaSF
Calls bg.correct at slaves.

Value

An AffyBatch for which the intensities have been background adjusted. For some methods (RMA), only PMs are corrected and the MMs remain the same.

Author(s)

Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann mansmann@ibe.med.uni-muenchen.de

Examples

## Not run: 
library(affyPara)
if (require(affydata)) {
  data(Dilution)

  c1 <- makeCluster(3)

  ##bgc will be the bg corrected version of Dilution 
  bgc <- bgCorrectPara(c1, Dilution, method="rma", verbose=TRUE)

  stopCluster(c1)
}
## End(Not run)

[Package affyPara version 1.2.1 Index]