gcrma {gcrma}R Documentation

Robust Multi-Array expression measure using sequence information

Description

This function converts an `AffyBatch' into an `exprSet' using the robust multi-array average (RMA) expression measure with help of probe sequence.

Usage

gcrma(object,estimate="eb",summary.method = "rlm",summary.subset=geneNames(object)[1:10]),...)

Arguments

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.

Details

Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

Value

An `exprSet'

Author(s)

Jean Wu, Rafeal Irizarry

References

Wei Shen and Thomas Louis. Triple-goal estimates in two-stage hierarchical models. J.R.Statist.Soc.B(1998)

Examples

require(affydata)
data(Dilution)
Dil.expr<-gcrma(Dilution,estimate="mle",summary.method = "medianpolish",summary.subset=geneNames(Dilution)[1:10])


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