vsnPara {affyPara} | R Documentation |
These parallel functions fit the vsn model to intensity data in an AffyBatch.
They hav the same functionality than the vsn methods in the vsn
package but are implemented in parallel (and only supports an AffyBatch as input data).
vsn2Para(object, phenoData = new("AnnotatedDataFrame"), cdfname = NULL, reference, subsample, ..., cluster, verbose = getOption("verbose")) justvsnPara(object, ..., cluster, verbose = getOption("verbose")) vsnrmaPara(object, pmcorrect.method="pmonly", pmcorrect.param=list(), summary.method="medianpolish", summary.param=list(), ids=NULL, phenoData = new("AnnotatedDataFrame"), cdfname = NULL, ..., cluster, verbose = getOption("verbose"))
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. |
subsample |
Integer of length 1. If specified, the model parameters are
estimated from a subsample of the data of size subsample
only, yet the fitted transformation is
then applied to all data. For large datasets, this can substantially
reduce the CPU time and memory consumption at a negligible loss of precision. |
reference |
Optional, a vsn object from
a previous fit. If this argument is specified, the data
are normalized "towards" an existing set of reference arrays whose
parameters are stored in the object reference . If this
argument is not specified, then the data are normalized
"among themselves". |
... |
Further arguments that get passed and are similar to vsn2 . |
cluster |
A cluster object obtained from the function makeCluster in the SNOW package.
For default .affyParaInternalEnv$cl will be used. |
verbose |
A logical value. If TRUE it writes out some messages. default: getOption("verbose") |
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 |
For the serial function and more details see the function vsn2
.
For using this function a computer cluster using the SNOW package has to be started.
Starting the cluster with the command makeCluster
generates an cluster object in the affyPara environment (.affyParaInternalEnv) and
no cluster object in the global environment. The cluster object in the affyPara environment will be used as default cluster object,
therefore no more cluster object handling is required.
The makeXXXcluster
functions from the package SNOW can be used to create an cluster object in the global environment and
to use it for the preprocessing functions.
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) makeCluster(3) AB1 <- justvsnPara(Dilution, verbose=verbose ) stopCluster() } ## End(Not run)