bgAdjustGcrma.AffymetrixCelSet {aroma.affymetrix}R Documentation

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

Returns the background adjusted AffymetrixCelFile object.

Author(s)

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

See Also

bg.adjust.gcrma For more information see AffymetrixCelSet.


[Package aroma.affymetrix version 1.2.0 Index]