normalizeAffyBatchConstantPara {affyPara} | R Documentation |
Parallelized scaling normalization of arrays.
normalizeAffyBatchConstantPara(cluster, object, refindex = 1, FUN = mean, na.rm = TRUE, phenoData = new("AnnotatedDataFrame"), cdfname = NULL, verbose = FALSE) normalizeConstantParaSF1(refindexname) normalizeConstantParaSF2(refconstant, refindexname, FUN = mean, na.rm = 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. |
refindex |
The index of the array used as reference. |
FUN |
A function generating a value from the intensities on an array. Typically mean or median . |
na.rm |
Paramater passed to the function FUN. A logical value indicating whether NA values should be stripped before the computation proceeds. |
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. |
refindexname |
The name of the array used as reference. |
refconstant |
The constant calculated by FUN from the reference array. This value will be used for scaling. |
Parallelized scaling normalization of arrays. This means that all the array are scaled so that they have the same mean value.
For the serial function and more details see the function normalize.constant
.
For using this function a computer cluster using the snow
package has to be started.
normalizeConstantParaSF1
and normalizeConstantParaSF2
are internal function which will be executed at all slaves.
normalizeConstantParaSF1
normalizeConstantParaSF2
An AffyBatch of normalized objects.
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) AffyBatch <- normalizeAffyBatchConstantPara(c1, Dilution, verbose=TRUE) stopCluster(c1) } ## End(Not run)