bg.adjust.gcrma {gcrma}R Documentation

Background ajustment with sequence information (internal function)

Description

An internal function to be used by bg.correct.gcrma.

Usage

bg.adjust.gcrma(Data, gcgroup, estimate = c("eb", "mle"), rho = 0.8, 
    step = 60, lower.bound = 1, baseline = 0.25,triple.goal, ...) 

Arguments

Data matrix of 2 columns, column 1: pm intensities,column 2: mm intensities.
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.
triple.goal
step a parameter in approximating "eb" estimates.
... extra arguments to pass to bg.adjust.

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

a vector of length nrow(Data).

Author(s)

Jean Wu, Rafeal Irizarry

See Also

bg.correct.gcrma


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