cn.farms (version 1.20.0)

normalizeNpData: Processes the non-polymorphic data

Description

Normalization for non-polymorphic data for Affymetrix SNP5 and SNP6

Usage

normalizeNpData(filenames, cores = 1, annotDir = NULL, runtype = "ff", saveFile = "npData", method = c("baseline", "quantiles", "none"))

Arguments

filenames

the absolute path of the CEL files as a list

cores

number of cores for used for parallelization

annotDir

Optional annotation directory.

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.

saveFile

Name of the file to save.

method

The method for the normalization.

Value

An instance of ExpressionSet containing the non-polymorphic data of the microarray.

Examples

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