fast.bkg: Internal functions for justGCRMA
In gcrma: Background Adjustment Using Sequence Information

Description Usage Arguments Details Value Author(s) See Also

These are internal functions for justGCRMA that are called based on memory or speed constraints.

fast.bkg(filenames, pm.affinities, mm.affinities, index.affinities,
type, minimum, optical.correct, verbose, k, rho, correction, stretch,
fast, cdfname, read.verbose)
mem.bkg(filenames, pm.affinities, mm.affinities, index.affinities, type,
minimum, optical.correct, verbose, k, rho, correction, stretch, fast,
cdfname, read.verbose)

`filenames`	A list of cel files.
`pm.affinities`	Values passed from `compute.affinities`.
`mm.affinities`	Values passed from `compute.affinities`.
`index.affinities`	Values passed from `compute.affinities`.
`type`	"fullmodel" for sequence and MM model. "affinities" for sequence information only. "mm" for using MM without sequence information.
`minimum`	A minimum value to be used for `optical.correct`.
`optical.correct`	Logical value. If `TRUE`, optical background correction is performed.
`verbose`	Logical value. If `TRUE`, messages about the progress of the function are printed.
`k`	A tuning factor.
`rho`	correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7
`correction`
`stretch`
`fast`	Logical value. If `TRUE`, then a faster ad hoc algorithm is used.
`cdfname`	Used to specify the name of an alternative cdf package. If set to `NULL`, the usual cdf package based on Affymetrix' mappings will be used. Note that the name should not include the 'cdf' on the end, and that the corresponding probe package is also required to be installed. If either package is missing an error will result.
`read.verbose`	Logical value. If `TRUE`, a message is returned as each celfile is read in.