cn.farms (version 1.20.0)

normalizeCels: Wrapper for the normalization functions

Description

This functions provides different normalization methods for microarray data. At the moment only SOR and quantile normalization are implemented.

Usage

normalizeCels(filenames, method = c("SOR", "quantiles", "none"), cores = 1, alleles = FALSE, runtype = "bm", annotDir = NULL, saveFile = "normData", ...)

Arguments

filenames

The absolute path of the CEL files as a list.

method

The normalization method. Possible methods so far: SOR, quantiles

cores

Number of cores for used for parallelization.

alleles

States if information for allele A and B should be given back.

runtype

Mode how the results are saved. Possible values are ff or bm. If ff is chosen the data will not be saved automatically. With bm the results will be saved permanently.

annotDir

An optional annotation directory.

saveFile

Name of the file to save.

...

Further parameters for the normalization method.

Value

An ExpressionSet object with the normalized data.

Examples

## Not run: 
# library("hapmapsnp6")
# celDir <- system.file("celFiles", package = "hapmapsnp6")
# filenames <- dir(path = celDir, full.names = TRUE)
# createAnnotation(filenames = filenames)
# normData <- normalizeCels(filenames, method = "SOR")
# ## End(Not run)