Scaling normalization

Description

Allows the user to apply scaling normalization.

Usage

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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

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