fast.bkg {gcrma} | R Documentation |
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 |
mm.affinities |
Values passed from |
index.affinities |
Values passed from |
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 |
Logical value. If |
verbose |
Logical value. If |
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 |
cdfname |
Used to specify the name of an alternative cdf package. If set to
|
read.verbose |
Logical value. If |
Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.
The tuning factor 'k' will have different meanings if one uses the fast (add-hoc) algorithm or the empirical Bayes approach. See Wu et al. (2003)
An ExpressionSet
.
James W. MacDonald <jmacdon@med.umich.edu>