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 `ExpressionSet`.

### Author(s)

Ben Bolstad, bmb@bmbolstad.com

### Examples

    if (require(affydata)) {
      data(Dilution)
      normalize.AffyBatch.scaling(Dilution)
    }

[Package affyPLM version 1.68.0 Index]