normalize.scaling {affyPLM} | R Documentation

## Scaling normalization

### Description

Allows the user to apply scaling normalization.

### Usage

    normalize.scaling(X,trim=0.02,baseline=-1,log.scalefactors=FALSE)
    normalize.AffyBatch.scaling(abatch,type=c("together","pmonly","mmonly","separate"),trim=0.02,baseline=-1,log.scalefactors=FALSE)

### Arguments

`X` | A matrix. The columns of which are to be normalized
`abatch` | An `AffyBatch`
`type` | A parameter controlling how normalization is applied to the Affybatch
`trim` | How much to trim from the top and bottom before computing the mean when using the scaling normalization
`baseline` | Index of array to use as baseline, negative values (-1,-2,-3,-4) control different baseline selection methods
`log.scalefactors` | Compute the scale factors based on log2 transformed data

### Details

These function carries out scaling normalization of expression values.

### Value

A normalized `exprSet`.

### Author(s)

Ben Bolstad, bmb@bmbolstad.com

### See Also

`normalize`

### Examples

    data(affybatch.example)
    normalize.AffyBatch.scaling(affybatch.example)

[Package affyPLM version 1.12.0 Index]