Starr (version 1.28.0)

normalize.Probes: Normalization of probes

Description

Normalization of probe intensities with a given method.

Usage

normalize.Probes(eSet, method=NULL, ratio=FALSE, ip, control, description, fkt=median, featureData=FALSE, targets=NULL, arrays = NULL, ...)

Arguments

eSet

An ExpressionSet, containing the logged raw intensities

method

character string specifying the normalization method to be used. Choices are "none", "scale", "quantile", "Aquantile", "Gquantile", "Rquantile", "Tquantile", "vsn", "rankpercentile", "loess", "substract".

ratio

if TRUE, the ratios are calcualted.

ip

a boolean vector, indicating which sample are IP experiments

control

a boolean vector, indicating which sample are CONTROL experiments

description

description of the normalized data

fkt

function to chose for averaging over replicates

featureData

should the featureData of eSet be passed to the new ExpressionSet?

targets

vector, factor or matrix of length twice the number of arrays, used to indicate target groups if method="Tquantile"

arrays

Subset of experiments (colnames in ExpressionSet) in the ExpressionSet, that are supposed to be normalized seperately.

...

arguments, that should be passed to the normalization methods.

Details

The procedure calls different functions from this package or from affy and limma, depending on the method.

none

Calls normalizeWithinArrays with method="none" from package limma.

scale

Calls normalizeWithinArrays with method="scale" from package limma.

quantile

Calls normalizeBetweenArrays with method="quantile" from package limma.

Gquantile

Calls normalizeBetweenArrays with method="Gquantile" from package limma.

Rquantile

Calls normalizeBetweenArrays with method="Rquantile" from package limma.

Tquantile

Calls normalizeBetweenArrays with method="Tquantile" from package limma.

Rquantile

Calls normalizeBetweenArrays with method="Rquantile" from package limma.

vsn

Calls normalizeBetweenArrays with method="vsn" from package limma.

loess

Calls normalize.loess from package affy.

rankpercentile

Calls rankPercentile.normalize from this package.

substract

Calls substract from this package.

See Also

normalizeBetweenArrays, normalize.loess , substract, rankPercentile.normalize

Examples

##
# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
# 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
# names <- c("rpb3_1", "wt_1","rpb3_2")
# type <- c("IP", "CONTROL", "IP")
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)

# rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")