standardNormalization {beadarraySNP} | R Documentation

## Default complete normalization

### Description

Performs all steps in normalization at best settings as determined in ref.

### Usage

    standardNormalization(snpdata)

### Arguments

`snpdata` | SnpSetIllumina object with raw data

### Details

The function performs in the following steps `snpdata<-normalizeBetweenAlleles.SNP(snpdata)`
`snpdata<-normalizeWithinArrays.SNP(snpdata,callscore = 0.8, relative = TRUE, fixed = FALSE, quantilepersample = TRUE)`
`snpdata<-normalizeLoci.SNP(snpdata,normalizeTo = 2)`

### Value

A `SnpSetIllumina` object with the `G, R and intensity` elements in assayData normalized to obtain values close to 2 on a linear scale for unaffected material.

### Author(s)

Jan Oosting

### See Also

`normalizeBetweenAlleles.SNP`,`normalizeWithinArrays.SNP`, `normalizeLoci.SNP`

### Examples

      data(chr17.260)
      data.nrm<-standardNormalization(chr17.260)

[Package beadarraySNP version 1.46.0 Index]