gcrma.engine {gcrma} | R Documentation |
This function adjust for non-specific binding when all arrays in the dataset share the same probe affinity information. It takes matrices of PM probe intensities, MM probe intensities, other negative control probe intensities(optional) and the associated probe affinities, and return one matrix of non-specific binding corrected PM probe intensities.
gcrma.engine(pms,mms,ncs=NULL, pm.affinities=NULL,mm.affinities=NULL,anc=NULL, 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=FALSE)
pms |
The matrix of PM intensities |
mms |
The matrix of MM intensities |
ncs |
The matrix of negative control probe intensities. When left
asNULL , the MMs are considered the negative control probes. |
pm.affinities |
The vector of PM probe affinities. Note: This can be
shorter than the number of rows in pms when some probes do not
have sequence information provided. |
mm.affinities |
The vector of MM probe affinities. |
anc |
The vector of Negative Control probe affinities. This is
ignored if MMs are used as negative controls (ncs=NULL ) |
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.engine2