bg.correct.gcrma {gcrma} | R Documentation |
Background corrects probe intensities in an object of class
AffyBatch
.
bg.correct.gcrma(object,gcgroup=getGroupInfo(Dilution)),...)
object |
An object of class AffyBatch . |
gcgroup |
A list of indexes indicating G,C strata. |
... |
estimate:method of background correction, "eb" for empirical Bayes, "mle" for maximum likelihood.
rho:correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.8. baseline:For estimate="mle" only. The lowest log(expression) value allowed. Default=.25 lower.bound:For estimate="eb" only. Lower bound of signal intensity allowed a priori. Default=1. |
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.
An AffyBatch
for which the PM
intensities have been background adjusted and MMs remain the
same.
Jean Wu, Rafeal Irizarry
require(affydata) data(Dilution) Dil.adj<-bg.correct.gcrma(Dilution,gcgroup=getGroupInfo(Dilution),estimate="mle")