normalizeBetweenAlleles.SNP {beadarraySNP} | R Documentation

## between Allele normalization

### Description

Perform between Allele normalization on Illumina Golden Gate bead arrays

### Usage

       normalizeBetweenAlleles.SNP(object,method=c("quantile"),subsample="OPA")

### Arguments

`object` | class `SnpSetIllumina`
`method` | `char`, type of normalization
`subsample` | `factor` with length number of features in object or `char`,column name in `featureData` slot

### Details

This function performs a quantile normalization between the Red and Green channels for each sample. The rationale for this procedure stems from the fact that the allele frequencies within each channel are always very similar, even in the presence of genomic abnormalities.

### Value

This function returns an `SnpSetIllumina` object.

### Author(s)

Jan Oosting

### See Also

`SnpSetIllumina-class`,`normalizeWithinArrays.SNP`, `backgroundCorrect.SNP`

### Examples

    data(chr17.260)
    data.nrm<-normalizeBetweenAlleles.SNP(chr17.260)

[Package beadarraySNP version 1.46.0 Index]