computeExprSetPara {affyPara} | R Documentation |
Parallel generation of a set of expression values from the probe pair information. The set of expression is returned as an ExpressionSet object.
computeExprSetPara(cluster, object, ids = NULL, pmcorrect.method, summary.method, summary.param = list(), pmcorrect.param = list(), phenoData = new("AnnotatedDataFrame"), cdfname = NULL, verbose = TRUE)
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. |
pmcorrect.method |
The name of the PM adjustement method. |
pmcorrect.param |
A list of parameters for pmcorrect.method (if needed/wanted). |
summary.method |
The method used for the computation of expression values |
summary.param |
A list of parameters to be passed to the summary.method (if wanted). |
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 in one steps: summarization
For the serial function and more details see the function computeExprSet
.
For using this function a computer cluster using the snow
package has to be started.
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) if (require(affydata)) { data(Dilution) c1 <- makeCluster(3) esset <- computeExprSetPara(cluster, Dilution, pmcorrect.method = "pmonly", summary.method = "avgdiff", verbose = TRUE) stopCluster(c1) } ## End(Not run)