aroma.affymetrix (version 2.11.1)

normalizeQuantile.AffymetrixCelFile: 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.

See Also

normalizeQuantile For more information see AffymetrixCelFile.