normalizeBetweenSubsamples.SNP: Normalization between subsamples

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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)

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.