normalizeQuantile.AffymetrixCelFile: Normalizes the probe intensities to a target empirical...

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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, Ken Simpson

See Also

normalizeQuantile For more information see AffymetrixCelFile.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.