gcrma {gcrma} | R Documentation |
This function converts an `AffyBatch' into an `exprSet' using the robust multi-array average (RMA) expression measure with help of probe sequence.
gcrma(object,estimate="eb",summary.method = "rlm",summary.subset=geneNames(object)[1:10]),...)
object |
an AffyBatch |
estimate |
"eb" or "mle". An character indicating background correction method. "eb" for empirical Bayes, "mle" for maximum likelihood |
summary.method |
"medianpolish" or "rlm". Method to extract the expression value of a probeset from background adjusted intensities. |
normalize |
logical value. If TRUE normalize data using
normalize.method (default as quantile normalization) |
rho |
correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.8 |
triple.goal |
|
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. |
step |
a parameter in approximating "eb" estimates. |
Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.
An `exprSet'
Jean Wu, Rafeal Irizarry
Wei Shen and Thomas Louis. Triple-goal estimates in two-stage hierarchical models. J.R.Statist.Soc.B(1998)
require(affydata) data(Dilution) Dil.expr<-gcrma(Dilution,estimate="mle",summary.method = "medianpolish",summary.subset=geneNames(Dilution)[1:10])