normalize.scaling: Scaling normalization

In affyPLM: Methods for fitting probe-level models

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, [e-mail]

Examples

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

affyPLM documentation built on Nov. 8, 2020, 6:53 p.m.