gcrma (version 2.44.0)

bg.adjust.affinities: Background adjustment with sequence information (internal function)

Description

An internal function to be used by gcrma.

Usage

bg.adjust.fullmodel(pms,mms,ncs=NULL,apm,amm,anc=NULL,index.affinities,k=6
* fast + 0.25 * (1 - fast),rho=.7,fast=FALSE)
bg.adjust.affinities(pms,ncs,apm,anc,index.affinities,k=6
* fast + 0.25 * (1 - fast),fast=FALSE,nomm=FALSE)

Arguments

pms

PM intensities after optical background correction, before non-specific-binding correction.

mms

MM intensities after optical background correction, before non-specific-binding correction.

ncs

Negative control probe intensities after optical background correction, before non-specific-binding correction. If ncs=NULL, the MM probes are considered the negative control probes.

index.affinities

The index of pms with known sequences. (For some types of arrays the sequences of a small subset of probes are not provided by Affymetrix.)

apm

Probe affinities for PM probes with known sequences.

amm

Probe affinities for MM probes with known sequences.

anc

Probe affinities for Negative control probes with known sequences. This is ignored when ncs=NULL.

rho

correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7

k

A tuning parameter. See details.

fast

Logical value. If TRUE a faster add-hoc algorithm is used.

nomm

Logical value indicating if MM intensities are available and will to be used to estimate background.

Value

Details

Assumes PM=background1+signal,mm=background2, (log(background1),log(background2))' follow bivariate normal distribution, signal distribution follows power law. bg.parameters.gcrma and sg.parameters.gcrma provide adhoc estimates of the parameters.

the original gcrma uses an empirical Bayes estimate. this requires a complicated numerical integration. An add-hoc method tries to imitate the empirical Bayes estimate with a PM-B but values of PM-B<k going to k. This can be thought as a shrunken MVUE. For more details see Wu et al. (2003).

See Also

gcrma