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aroma.affymetrix (version 1.5.0)

bgAdjustGcrma.AffymetrixCelSet: Applies probe sequence based background correction to a set of CEL files

Description

Applies probe sequence based background correction to a set of CEL files. Adapted from bg.adjust.gcrma in the gcrma package.

Usage

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

Arguments

path
The path where to save the adjusted data files.
name
Name of the set containing the background corrected 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.
opticalAdjust
If TRUE, apply correction for optical effect, as in bg.adjust.optical.
gsbAdjust
Should we adjust for specific binding (defaults to TRUE)?
k
Tuning parameter passed to gcrma::bg.adjust.gcrma.
rho
Tuning parameter passed to gcrma::bg.adjust.gcrma.
stretch
Tuning parameter passed to gcrma::bg.adjust.gcrma.
fast
If TRUE, an ad hoc transformation of the PM is performed (gcrma::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

See Also

bg.adjust.gcrma For more information see AffymetrixCelSet.