bg.correct.gcrma {gcrma}R Documentation

Background Correction Using sequence information

Description

Background corrects probe intensities in an object of class AffyBatch.

Usage

bg.correct.gcrma(object,gcgroup=getGroupInfo(Dilution)),...)

Arguments

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.

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.

Value

An AffyBatch for which the PM intensities have been background adjusted and MMs remain the same.

Author(s)

Jean Wu, Rafeal Irizarry

Examples

 require(affydata)
data(Dilution)
Dil.adj<-bg.correct.gcrma(Dilution,gcgroup=getGroupInfo(Dilution),estimate="mle")

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