fast.bkg {gcrma}R Documentation

Internal functions for justGCRMA

Description

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

Usage

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)

Arguments

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.

Details

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)

Value

An exprSet.

Author(s)

James W. MacDonald <jmacdon@med.umich.edu>

See Also

gcrma


[Package gcrma version 1.1.0 Index]