preproPara {affyPara} | R Documentation |
Parallelized preprocessing function, which goes from raw probe intensities to expression values in three steps: Background correction, normalization and summarization
preproPara(object, bgcorrect = TRUE, bgcorrect.method = NULL, bgcorrect.param = list(), normalize = TRUE, normalize.method = NULL, normalize.param = list(), pmcorrect.method = NULL, pmcorrect.param = list(), summary.method = NULL, 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. |
bgcorrect |
A boolean to express whether background correction is wanted or not. |
bgcorrect.method |
The name of the background adjustment method to use. |
bgcorrect.param |
A list of parameters for bgcorrect.method (if needed/wanted) |
normalize |
A boolean to express whether normalization is wanted or not. |
normalize.method |
The name of the normalization method to use. |
normalize.param |
A list of parameters to be passed to the normalization method (if wanted). |
pmcorrect.method |
The name of the PM adjustment 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. |
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") |
Parallelized preprocessing function, which goes from raw probe intensities to expression values in three steps: Background correction, normalization and summarization
For the serial function and more details see the function expresso
.
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.
Available methods:
bgcorrect.method
:bgcorrect.methods()
normalize.method
:summary.method
:generateExprSet.methods()
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) makeCluster(3) esset <- preproPara(Dilution, bgcorrect = TRUE, bgcorrect.method = "rma2", normalize = TRUE, normalize.method = "quantil", pmcorrect.method = "pmonly", summary.method = "avgdiff", verbose = TRUE) stopCluster() } ## End(Not run)