gcrma.engine2 {gcrma}R Documentation

GCRMA background adjust engine(internal function)

Description

This function adjust for non-specific binding when each array has its own probe affinity information. It takes an AffyBatch object of probe intensities and an AffyBatch of probe affinity, returns one matrix of non-specific binding corrected PM probe intensities.

Usage

gcrma.engine2(object,pmIndex=NULL,mmIndex=NULL,
              NCprobe=NULL,affinity.info,
              type=c("fullmodel","affinities","mm","constant"),
              k=6*fast+0.5*(1-fast),
              stretch=1.15*fast+1*(1-fast),correction=1,GSB.adjust=TRUE,rho=0.7,
              verbose=TRUE,fast=TRUE)

Arguments

object an AffyBatch. Note: this is an internal function. Optical noise should have been corrected for.
pmIndex Index of PM probes.This will be computed within the function if left NULL
mmIndex Index of MM probes.This will be computed within the function if left NULL
NCprobe
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.
stretch
correction .
GSB.adjust Logical value. If TRUE, probe effects in specific binding will be adjusted.
rho correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7
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

A matrix of PM intensties.

Author(s)

Rafeal Irizarry & Zhijin Wu

See Also

gcrma.engine

Examples






[Package gcrma version 2.2.0 Index]