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(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)
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. |
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
: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) c1 <- makeCluster(3) esset <- preproPara(cluster, Dilution, bgcorrect = TRUE, bgcorrect.method = "rma2", normalize = TRUE, normalize.method = "quantil", pmcorrect.method = "pmonly", summary.method = "avgdiff", verbose = TRUE) stopCluster(c1) } ## End(Not run)