normalizeQuantile.AffymetrixCelFile {aroma.affymetrix}R Documentation

Normalizes the probe intensities to a target empirical distribution

Description

Normalizes the probe intensities to a target empirical distribution.

Usage

## S3 method for class 'AffymetrixCelFile':
normalizeQuantile(this, path=file.path("normQuantile", getChipType(this)), xTarget, subsetToUpdate=NULL, typesToUpdate=NULL, ..., overwrite=FALSE, skip=!overwrite, verbose=FALSE)

Arguments

path The path where to save the normalized data files.
xTarget A numeric vector. The empirical distribution to which all arrays should be normalized to.
subsetToUpdate The indices of the probes to be updated. If NULL, all are updated.
typesToUpdate Types of probes to be updated. For more details, see argument types of identifyCells() for the AffymetrixCdfFile class.
... Additional arguments passed to normalizeQuantile().
overwrite If TRUE, already normalized arrays are overwritten, unless skipped, otherwise an error is thrown.
skip If TRUE, the array is not normalized if it already exists.
verbose See Verbose.

Value

Returns the normalized AffymetrixCelFile object.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

normalizeQuantile.numeric For more information see AffymetrixCelFile.


[Package aroma.affymetrix version 1.2.0 Index]