gcrma.engine2 {gcrma}  R Documentation 
This function adjust for nonspecific 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 nonspecific binding corrected PM probe intensities.
gcrma.engine2(object,pmIndex=NULL,mmIndex=NULL, NCprobe=NULL,affinity.info, type=c("fullmodel","affinities","mm","constant"), k=6*fast+0.5*(1fast), stretch=1.15*fast+1*(1fast),correction=1,GSB.adjust=TRUE,rho=0.7, verbose=TRUE,fast=TRUE)
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 addhoc algorithm is
used. 
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 (addhoc) algorithm or the empirical bayes approach. See Wu
et al. (2003)
A matrix of PM intensties.
Rafeal Irizarry & Zhijin Wu
gcrma.engine