normalize.Probes: Normalization of probes
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Details Author(s) See Also Examples

Normalization of probe intensities with a given method.

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

`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.

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.

Benedikt Zacher zacher@lmb.uni-muenchen.de

normalizeBetweenArrays, normalize.loess , substract, rankPercentile.normalize

##
# 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")