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gcrma (version 2.44.0)

gcrma.engine2: 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
Index of negative control probes. When set as NULL,the MM probes will be used. These probes are used to estimate parameters of non-specific binding on each array. These will be also used to estimate probe affinity profiles when affinity.info is not provided.
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.

Value

A matrix of PM intensties.

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)

See Also

gcrma.engine