getBackground {ARRmNormalization} | R Documentation

## Estimate background intensity from the negative control probes

### Description

This function estimates background intensity for the two colors by taking the median of the negative control probes in each color channel.

### Usage

    getBackground(greenControlMatrix, redControlMatrix)

### Arguments

`greenControlMatrix` | matrix of negative control probes intensities in the green channel. Rows are probes, columns are samples.
`redControlMatrix` | matrix of the negative control probes intensities in the red channel. Rows are probes, columns are samples.

### Value

Returns a `data.frame` with two columns; `"green"` contains the background intensity in the green channel for each sample and `"red"` contains the background intensity in the red channel for each sample

### Author(s)

Jean-Philippe Fortin <jfortin@jhsph.edu>

### Examples

    data(greenControlMatrix)
    data(redControlMatrix)
    getBackground(greenControlMatrix,redControlMatrix)

[Package ARRmNormalization version 1.20.0 Index]