normalizeAffyBatchQuantilesPara {affyPara} | R Documentation |
Parallelized normalization of arrays based upon quantiles.
normalizeAffyBatchQuantilesPara(cluster, object, phenoData = new("AnnotatedDataFrame"), cdfname = NULL, type = c("separate", "pmonly", "mmonly", "together"), verbose = FALSE) normalizeQuantilesPara(cluster, type, object.length, verbose=FALSE) normalizeQuantilesParaSF1(type) normalizeQuantilesParaSF2(row_mean)
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. |
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. |
type |
A string specifying how the normalization should be applied. |
verbose |
A logical value. If TRUE it writes out some messages. |
object.length |
Number of samples, which should be normalized. |
row_mean |
Row mean used for normalization. |
Parallelized normalization of arrays based upon quantiles. This method is based upon the concept of a quantile-quantile plot extended to n
dimensions. No special allowances are made for outliers.
For the serial function and more details see the function normalize.AffyBatch.quantiles
.
For using this function a computer cluster using the snow
package has to be started.
normalizeQuantilesPara
, normalizeQuantilesParaSF1
and normalizeQuantilesParaSF2
are internal function which will be executed at all slaves.
normalizeQuantilesPara
normalizeQuantilesParaSF1
normalizeQuantilesParaSF2
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 <- normalizeAffyBatchQuantilesPara(c1, Dilution, verbose=TRUE) stopCluster(c1) } ## End(Not run)