bg.adjust.affinities {gcrma} | R Documentation |
An internal function to be used by gcrma
.
bg.adjust.affinities(x,affinities,index=seq(along=x),k,Q=0.25,fast=TRUE)
x |
PM intensities after optical background correction, before non-specific-binding correction. |
index |
The index of x with known sequences. (For some types of arrays the sequences of a small subset of probes are not provided by Affymetrix.) |
affinities |
Probe affinities for probes with known sequences. |
k |
A tuning parameter. See details |
Q |
A number between 0 and 1 that determines what quantile to use as an estimate of the mean background noise. |
fast |
Logical value. If TRUE a faster add-hoc algorithm is
used. |
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 emprical bayes estimate. this requiers a
complicated numerical integration. An add-hoc method tries to immitate
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