backgroundCorrect2: Background correction

In OLIN: Optimized local intensity-dependent normalisation of two-color microarrays

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:

• “none”: no background correction

• “subtract”: simple subtraction of background intensities

• “movingmin”: background intensities are first averaged over 3x3 grids of neighbouring spots and subsequently substracted

• “minimum”: zero or negative intensities after background correction are set equal to half the minimum of positive corrected intensities

• “edwards”: background correction based on log-linear interpolation

• “normexp”: background correction based on fitting procedure

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")
 

OLIN documentation built on Nov. 8, 2020, 7:44 p.m.