ARRmNormalization (version 1.12.0)

getBackground: 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

Examples

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