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aroma.affymetrix (version 2.2.0)

bgAdjustGcrma.AffymetrixCelFile: 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=c("fullmodel", "affinities"), indicesNegativeControl=NULL, affinities=NULL, gsbAdjust=TRUE, parametersGsb=NULL, k=ifelse(fast, 6, 0.5), rho=0.7, stretch=ifelse(fast, 1.15, 1), 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", then MMs are used as the negative con
affinities
A numeric vector of probe affinities, usually as calculated by computeAffinities() of the
gsbAdjust
If TRUE, adjustment for specific binding is done, otherwise not.
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

See Also

bg.adjust.gcrma For more information see AffymetrixCelFile.