OLIN (version 1.50.0)

backgroundCorrect2: 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

Value

marrayRaw.

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.

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")