normalize.Probes {Starr} | R Documentation

## 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.

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### 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")

[Package Starr version 1.42.0 Index]