preproPara {affyPara}R Documentation

Parallelized preprocessing

Description

Parallelized preprocessing function, which goes from raw probe intensities to expression values in three steps: Background correction, normalization and summarization

Usage

preproPara(cluster,
    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,
    verbose = FALSE)

Arguments

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.
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 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.

Details

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.

Available methods:

bgcorrect.method:
see bgcorrect.methods
normalize.method:
'quantil', 'constant', 'invariantset'
summary.method:
see generateExprSet.methods

Value

An object of class ExpressionSet.

Author(s)

Markus Schmidberger schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann mansmann@ibe.med.uni-muenchen.de

Examples

## Not run: 
library(affyPara)

data(affybatch.example)

c1 <- makeCluster(3)

esset <- preproPara(cluster,
    affybatch.example,
    bgcorrect = TRUE, bgcorrect.method = "rma2",
    normalize = TRUE, normalize.method = "quantil",
    pmcorrect.method = "pmonly",
    summary.method = "avgdiff",
    verbose = TRUE)
    
stopCluster(c1)
## End(Not run)

[Package affyPara version 1.0.0 Index]