normalize-methods {affy} | R Documentation

## Normalize Affymetrix Probe Level Data - methods

### Description

Method for normalizing Affymetrix Probe Level Data

### Usage

    normalize.methods(object)
    bgcorrect.methods()
    upDate.bgcorrect.methods(x)
    pmcorrect.methods()
    upDate.pmcorrect.methods(x)

### Arguments

`object` | An `AffyBatch`.
`x` | A character vector that will replace the existing one.

### Details

If `object` is an `AffyBatch` object, then `normalize(object)` returns an `AffyBatch` object with the intensities normalized using the methodology specified by `getOption("BioC")$affy$normalize.method`. The affy package default is `quantiles`.

Other methodologies can be used by specifying them with the `method` argument. For example to use the invariant set methodology described by Li and Wong (2001) one would type: `normalize(object, method="invariantset")`.

Further arguments passed by `...`, apart from `method`, are passed along to the function responsible for the methodology defined by the `method` argument.

A character vector of nicknames for the methodologies available is returned by `normalize.methods(object))`, where `object` is an `AffyBatch`, or simply by typing `normalize.AffyBatch.methods`. If the nickname of a method is called "loess", the help page for that specific methodology can be accessed by typing `?normalize.loess`.

For more on the normalization methodologies currently implemented please refer to the vignette ‘Custom Processing Methods’.

To add your own normalization procedures please refer to the customMethods vignette.

The functions: `bgcorrect.methods`, `pmcorrect.methods`, provide access to internal vectors listing the corresponding capabilities.

### See Also

`AffyBatch-class`, `normalize`.

### Examples

    if (require(affydata)) {
      data(Dilution)
      normalize.methods(Dilution)
      generateExprSet.methods()
      bgcorrect.methods()
      pmcorrect.methods()
    }

[Package affy version 1.68.0 Index]