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bgAdjustOptical.AffymetrixCelSet {aroma.affymetrix}

Applies optical background correction to a set of CEL files
Package: 
aroma.affymetrix
Version: 
2.2.0

Description

Applies optical background correction to a set of CEL files.

Adapted from bg.adjust.optical in the gcrma package.

Usage

 
## S3 method for class 'AffymetrixCelSet':
bgAdjustOptical((this, path=NULL, name="bgOptical", subsetToUpdate=NULL, typesToUpdate=NULL, minimum=1, overwrite=FALSE, skip=!overwrite, ..., verbose=FALSE, .deprecated=TRUE))

Arguments

path
The location to save the adjusted data files.
minimum
The minimum adjusted intensity. Defaults to 1.
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.
...
Not used.
overwrite
If TRUE, already adjusted 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.
.deprecated
Internal argument.

Values

Returns the background adjusted AffymetrixCelSet object.

Author(s)

Ken Simpson (ksimpson[at]wehi.edu.au).

Documentation reproduced from package aroma.affymetrix, version 2.2.0. License: LGPL (>= 2.1)