bgAdjustOptical.AffymetrixCelFile {aroma.affymetrix}R Documentation

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=file.path("bgOptical", getChipType(this)), 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.

Author(s)

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


[Package aroma.affymetrix version 1.2.0 Index]