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) mem.bkg(filenames, pm.affinities, mm.affinities, index.affinities, type, minimum, optical.correct, verbose, k, rho, correction, stretch, fast)
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. |
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 tunning 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 exprSet
.
James W. MacDonald <jmacdon@med.umich.edu>