rmaPara {affyPara} | R Documentation |
Parallelized preprocessing function, which converts an AffyBatch into an ExpressionSet using the robust multi-array average (RMA) expression measure.
rmaPara(cluster, object, ids = NULL, phenoData = new("AnnotatedDataFrame"), cdfname = NULL, verbose=FALSE)
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. |
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
.
An object of class ExpressionSet.
Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann mansmann@ibe.med.uni-muenchen.de
## Not run: library(affyPara) data(affybatch.example) c1 <- makeCluster(3) esset <- rmaPara(cluster, affybatch.example) stopCluster(c1) ## End(Not run)