gcrma.engine2 {gcrma} | R Documentation |
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.
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)
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. |
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)
A matrix of PM intensties.
Rafeal Irizarry & Zhijin Wu
gcrma.engine