normalizeCels: Wrapper for the normalization functions

In cn.farms: cn.FARMS - factor analysis for copy number estimation

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.

Author(s)

Djork-Arne Clevert [e-mail] and Andreas Mitterecker [e-mail]

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)

cn.farms documentation built on Nov. 8, 2020, 7:59 p.m.