bgAdjustGcrma.AffymetrixCelFile {aroma.affymetrix}R Documentation

Applies probe sequence based background correction to a CEL file

Description

Applies probe sequence based background correction to a CEL file.

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

Usage

## S3 method for class 'AffymetrixCelFile':
bgAdjustGcrma(this, path=NULL, type="fullmodel", indicesNegativeControl=NULL, affinities=NULL, gsbAdjust=TRUE, parametersGsb=NULL, k=6 * fast + 0.5 * (1 - fast), rho=0.7, stretch=1.15 * fast + 1 * (1 - fast), fast=TRUE, overwrite=FALSE, skip=!overwrite, ..., verbose=FALSE, .deprecated=TRUE)

Arguments

path The path where to save the adjusted data files.
type The type of background correction. Currently accepted types are "fullmodel" (the default, uses MMs) and "affinities" (uses probe sequence only).
indicesNegativeControl Locations of any negative control probes (e.g., the anti-genomic controls on the human exon array). If NULL and type=="affinities", MMs are used as the negative controls.
affinities A numeric vector of probe affinities, usually as calculated by computeAffinities() of the AffymetrixCdfFile class.
gsbAdjust Should we adjust for specific binding (defaults to TRUE)?
parametersGsb Specific binding parameters as estimated by calculateParametersGsb() for the AffymetrixCelSet class.
k Tuning parameter passed to bg.adjust.gcrma.
rho Tuning parameter passed to bg.adjust.gcrma.
stretch Tuning parameter passed to bg.adjust.gcrma.
fast If TRUE, an ad hoc transformation of the PM is performed (gcrma.bg.transformation.fast()).
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) and Mark Robinson.

See Also

bg.adjust.gcrma For more information see AffymetrixCelFile.


[Package aroma.affymetrix version 1.2.0 Index]