Usage
preproPara(object, cluster, 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 = getOption("verbose"), ...)
Arguments
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
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")
...
Further arguments that get passed to the affyBatch creation process.