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,affinity.info=NULL,
                  type=c("fullmodel","affinities","mm","constant"),
                  k=6*fast+0.5*(1-fast),stretch=1.15*fast+1*(1-fast),correction=1,
                  rho=.7,optical.correct=TRUE,verbose=TRUE,fast=TRUE)

Arguments

object an AffyBatch
affinity.info NULL or an AffyBatch containing the affinities in the exprs slot. This object can be created using the function compute.affinities.
type "fullmodel" for sequence and MM model. "affinities" for sequence information only. "mm" for using MM without sequence information.
k A tuning factor.
rho correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7
stretch
correction .
optical.correct Logical value. If TRUE, optical background correction is performed.
verbose Logical value. If TRUE messages about the progress of the function is printed.
fast Logicalvalue. If TRUE a faster add-hoc algorithm is used.

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.

The tunning factor k will have different meainngs if one uses the fast (add-hoc) algorithm or the empirical bayes approach. See Wu et al. (2003)

Value

An exprSet.

Author(s)

Rafeal Irizarry

Examples

if(require(affydata) & require(hgu95av2probe)){
     data(Dilution)
     ai <- compute.affinities(cdfName(Dilution))
     Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities")
}

[Package gcrma version 1.1.0 Index]