normalization: normalization

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

Function that normalizes raw data.

Usage

normalization(my.data = NULL, method = NULL, targetsinfo, inputDir,
  loadFile = FALSE, normalizedFName = "normalized.Rda", outputDir,
  exonSt = FALSE)

Arguments

my.data	Raw data to be normalized.
method	Method used for the normalization.
targetsinfo	Target information about raw data.
inputDir	Path of the normalized data file.
loadFile	If TRUE the normalized data is loaded.
normalizedFName	Name of the eset normalized file. By default "normalized.Rda"
outputDir	Path to store the raw data normalized.
exonSt	Default value FALSE. If TRUE the raw data is exon array.

Value

A data set called my.norm with the raw data normalized.

Examples

## Not run: 
load("rawData.Rda")
rawData <- my.raw
normMethod <- "RMA"
my.targets <- read.AnnotatedDataFrame("./celfiles/targets.txt", header = TRUE, row.names = 1)
celFilesDir <-"./celfiles"
loadFile <- FALSE
normalized.eset.FileName <-  "normalizedData.Rda"
outputDir <- "./ResultsDir"
exonStudy <- FALSE
eset_norm <- normalization(my.data = rawData, method = normMethod,
targetsinfo = my.targets, inputDir = celFilesDir, loadFile = loadFile ,
normalizedFName = normalized.eset.FileName, outputDir = outputDir,
exonSt = exonStudy)
## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.