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:

- “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")

[Package OLIN version 1.12.0 Index]