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Home » Package reference » aroma.affymetrix » normalizeQuantile.AffymetrixCelSet {aroma.affymetrix}

normalizeQuantile.AffymetrixCelSet {aroma.affymetrix}

Normalizes samples to have the same empirical distribution
Package: 
aroma.affymetrix
Version: 
2.9.0

Description

Normalizes samples to have the same empirical distribution.

Usage

 
## S3 method for class 'AffymetrixCelSet':
normalizeQuantile((this, path=NULL, name="normQuantile", subsetToUpdate=NULL, typesToUpdate=NULL, xTarget=NULL, subsetToAvg=subsetToUpdate, typesToAvg=typesToUpdate, ..., verbose=FALSE))

Arguments

path
The path where to save the normalized data files. If NULL, a default name is used.
name
The name of the normalized data set, which will also be part of the default path.
subsetToUpdate
The probes to be updated. If NULL, all probes are updated.
typesToUpdate
Types of probes to be updated.
xTarget
A numeric vector. The empirical distribution to which all arrays should be normalized to.
subsetToAvg
The probes to calculate average empirical distribution over. If a single numeric in (0,1), then this fraction of all probes will be used. If NULL, all probes are considered.
typesToAvg
Types of probes to be used when calculating the average empirical distribution. If "pm" and "mm" only perfect-match and mismatch probes are used, respectively. If "pmmm" both types are used.
...
Additional arguments passed to normalizeQuantile().
verbose
See Verbose.

Values

Returns a double vector.

See Also

normalizeQuantileRank.numeric For more information see AffymetrixCelSet.

Author(s)

Henrik Bengtsson

Documentation reproduced from package aroma.affymetrix, version 2.9.0. License: LGPL (>= 2.1)