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

See Also

normalize

Examples

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

[Package affyPLM version 1.16.0 Index]