bg.adjust.affinities: Background adjustment with sequence information (internal...
In gcrma: Background Adjustment Using Sequence Information

Description Usage Arguments Details Value Author(s) See Also

An internal function to be used by gcrma.

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)

`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.

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).

a vector of same length as x.

Rafeal Irizarry, Zhijin(Jean) Wu

gcrma

gcrma documentation built on Nov. 8, 2020, 5:12 p.m.