affy (version 1.50.0)

normalize.scaling: 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
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.

Value

Details

These function carries out scaling normalization of expression values.

Examples

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

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