bgAdjustOptical.AffymetrixCelFile {aroma.affymetrix} | R Documentation |
Applies optical background correction to a CEL file.
Adapted from bg.adjust.optical
in the gcrma package.
## S3 method for class 'AffymetrixCelFile': bgAdjustOptical(this, path=file.path("bgOptical", getChipType(this)), minimum=1, subsetToUpdate=NULL, typesToUpdate=NULL, overwrite=FALSE, skip=!overwrite, verbose=FALSE, ..., .deprecated=TRUE)
path |
The location to save the adjusted data files. |
minimum |
The minimum adjusted intensity. Defaults to 1. |
subsetToUpdate |
The indices of the probes to be updated.
If NULL , all are updated. |
typesToUpdate |
Types of probes to be updated. For more details,
see argument types of identifyCells() for the
AffymetrixCdfFile class. |
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).