rmaPara {affyPara}R Documentation

Parallelized PMA preprocessing

Description

Parallelized preprocessing function, which converts an AffyBatch into an ExpressionSet using the robust multi-array average (RMA) expression measure.

Usage

rmaPara(cluster,
        object,
        ids = NULL,
        phenoData = new("AnnotatedDataFrame"), cdfname = NULL,
        verbose=FALSE)

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.
ids List of ids for summarization
phenoData An AnnotatedDataFrame object.
cdfname Used to specify the name of an alternative cdf package. If set to NULL, the usual cdf package based on Affymetrix' mappings will be used.
verbose A logical value. If TRUE it writes out some messages.

Details

Parallelized preprocessing function, which goes from raw probe intensities to expression values using the robust multi-array average (RMA) expression measure: Background correction: rma; Normalization: quantile; Summarization: medianpolish

For the serial function and more details see the function rma.

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

This is a wrapper function for preproPara.

Value

An object of class ExpressionSet.

Author(s)

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

Examples

## Not run: 
library(affyPara)

data(affybatch.example)

c1 <- makeCluster(3)

esset <- rmaPara(cluster, affybatch.example)
    
stopCluster(c1)
## End(Not run)

[Package affyPara version 1.0.0 Index]