normalize.scaling {affyPLM}R Documentation

Scaling normalization

Description

Allows the user to apply scaling normalization.

Usage

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

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

Details

These function carries out scaling normalization of expression values.

Value

A normalized exprSet.

Author(s)

Ben Bolstad, bolstad@stat.berkeley.edu

See Also

normalize

Examples

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

[Package affyPLM version 1.6.0 Index]