backgroundEstimate: Estimate background intensities from foreground intensity

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Background intensity from Illumina Golden Gate bead arrays are estimated based on several data models

Usage

  backgroundEstimate(object,method=c("minimum", "mode","intmin", 
  "anglemode"), maxmode=3000, bincount=40, maxangle=0.3, subsample="OPA")

Arguments

object	SnpSetIllumina object
method	chracter, data model to use
maxmode	numeric, maximum intensity for mode for method="mode"
bincount	numeric, for method="intmin" , see details
maxangle	numeric in radians, maximum theta for mode for method="anglemode"
subsample	factor or column name in featureData slot

Details

The Illumina software does not provide background values in the output. Some models can be used to estimate background from the raw data intensities.
minimum: The allele specific minimum intensity is used.
mode: This model assumes that the first mode of the density of the intensities is determined by the zero-allele in the data, see ref. The signal intensity of the zero-allele should be zero, therefore this is considered the background value.
intmin: This model assumes there is crosstalk between the alleles, and background increases with the intensity of the other allele. The range between 0 and the maximum of the other allele is divided in bincount bins, and the minimum for this allele is determined for probes where the other allele falls in a bin. A linear fit is determined though the minimum values to obtain a gradually increasing value.
anglemode: This model finds the density modes closest to 0 and \frac{π}{2} for polar transformed intensities, and uses this to determine background.

Value

This function returns an SnpSetIllumina object. The Rb and Gb matrices in the assayData slot contain estimated background values.

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class, backgroundCorrect.SNP

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