bg.adjust.gcrma {gcrma} | R Documentation |
An internal function to be used by bg.correct.gcrma
.
bg.adjust.gcrma(Data, gcgroup, estimate = c("eb", "mle"), rho = 0.8, step = 60, lower.bound = 1, baseline = 0.25,triple.goal, ...)
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. |
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.
a vector of length nrow(Data).
Jean Wu, Rafeal Irizarry