| 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)
data(affybatch.example)
c1 <- makeCluster(3)
esset <- computeExprSetPara(cluster,
affybatch.example,
pmcorrect.method = "pmonly",
summary.method = "avgdiff",
verbose = TRUE)
stopCluster(c1)
## End(Not run)