backgroundCorrect2 {OLIN}R Documentation

Background correction

Description

Background correction based on backgroundCorrect of the limma package.

Usage

backgroundCorrect2(object,method="subtract", offset=0)

Arguments

object object of class marrayRaw
method method for background correction: “none”, “subtract”, “half”, “minimum”, “movingmin”, “edwards” or “normexp”.
offset

{numeric value to add to intensities}

Details

This function is a wrapper function for backgroundCorrect with following methods implemented:

For further details and references, please refer to its help page. An alternative Bayesian model for background correction (kooperberg) is also implemented in the limma package.

Value

Background correct object of class marrayRaw.

Author(s)

Matthias Futschik

See Also

backgroundCorrect,kooperberg

Examples


# Loading data
data(sw)

#No background correction
  sw.none <- backgroundCorrect2(sw,method="none")
  plot(maA(sw.none)[,1],maM(sw.none)[,1])

# Simple subtraction
  sw.sub <- backgroundCorrect2(sw,method="sub")
  points(maA(sw.sub)[,1],maM(sw.sub)[,1],col="red")
 

[Package OLIN version 1.18.0 Index]