bg.correct {affy} | R Documentation

## Background Correction

### Description

Background corrects probe intensities in an object of class `AffyBatch`.

### Usage

    bg.correct(object, method, ...)

    bg.correct.rma(object,...)
    bg.correct.mas(object, griddim)
    bg.correct.none(object, ...)

### Arguments

`object` | An object of class `AffyBatch`.
`method` | A `character` that defines what background correction method will be used. Available methods are given by `bg.correct.methods`.
`griddim` | grid dimension used for mas background estimate. The array is divided into griddim equal parts. Default is 16.
`...` | arguments to pass along to the engine function.

### Details

The name of the method to apply must be double-quoted. Methods provided with the package are currently:

- bg.correct.none: returns `object` unchanged.

- bg.correct.chipwide: noise correction as described in a ‘white paper’ from Affymetrix.

- bg.correct.rma: the model based correction used by the RMA expression measure.

They are listed in the variable `bg.correct.methods`. The user must supply the word after "bg.correct", i.e none, subtractmm, rma, etc...

More details are available in the vignette.

R implementations similar in function to the internal implementation used by `bg.correct.rma` are in `bg.adjust`.

### Value

An `AffyBatch` for which the intensities have been background adjusted. For some methods (RMA), only PMs are corrected and the MMs remain the same.

### Examples

    if (require(affydata)) {
      data(Dilution)

      ##bgc will be the bg corrected version of Dilution
      bgc <- bg.correct(Dilution, method="rma")

      ##This plot shows the tranformation
      plot(pm(Dilution)[,1],pm(bgc)[,1],log="xy",
      main="PMs before and after background correction")
    }

[Package affy version 1.72.0 Index]