normalizeBetweenSubsamples.SNP {beadarraySNP} | R Documentation

## Normalization between subsamples

### Description

Quantile normalization between subsamples within a single SnpSetIllumina object

### Usage

    normalizeBetweenSubsamples.SNP(object, subsample = "OPA")

### Arguments

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

### Details

Perform quantile normalization of the red and green channel between subsamples. This can be used in situations where multiple different assays that cover the same genomic regions (or whole genome) have been done on the same biological specimen. This function was introduced for version 5 Golden Gate Linkage analysis that consist of 4 assays of ~ 1500 probes. Where previous versions of this assay each targeted a number of chromosomes, in version 5 each assay covers the whole genome.

### Value

This function returns an `SnpSetIllumina` object.

### Author(s)

Jan Oosting

### See Also

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

### Examples

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

[Package beadarraySNP version 1.53.0 Index]