gcrma.engine: GCRMA background adjust engine(internal function)
In gcrma: Background Adjustment Using Sequence Information

Description Usage Arguments Details Value Author(s) See Also

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 as`NULL`, 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.