aroma.affymetrix (version 2.11.1)

bgAdjustOptical.AffymetrixCelFile: Applies optical background correction to a CEL file

Description

Applies optical background correction to a CEL file.

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

Usage

## S3 method for class 'AffymetrixCelFile':
bgAdjustOptical(this, path, minimum=1, subsetToUpdate=NULL, typesToUpdate=NULL,
  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.

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.

Value

• Returns the background adjusted AffymetrixCelFile object.