bgAdjustGcrma.AffymetrixCelFile {aroma.affymetrix} | R Documentation |
Applies probe sequence based background correction to a CEL file.
Adapted from bg.adjust.gcrma
in the gcrma package.
## 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)
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. |
Returns the background adjusted AffymetrixCelFile
object.
Ken Simpson (ksimpson[at]wehi.edu.au) and Mark Robinson.
bg.adjust.gcrma
For more information see AffymetrixCelFile
.