aroma.affymetrix (version 3.2.2)

normalizeQuantile.AffymetrixCelSet: Normalizes samples to have the same empirical distribution

Description

Normalizes samples to have the same empirical distribution.

Usage

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

Value

Returns a double

vector.

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.

Author

Henrik Bengtsson

See Also

normalizeQuantileRank.numeric For more information see AffymetrixCelSet.