backgroundEstimate {beadarraySNP} | R Documentation

## Estimate background intensities from foreground intensity

### 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`

[Package beadarraySNP version 1.52.0 Index]