bg.adjust.gcrma {gcrma} | R Documentation |
This function performs background adjustment (optical noise and
non-specific binding on an AffyBatch
project and returns an AffyBatch
object in which the PM
intensities are adjusted.
bg.adjust.gcrma(object,affinity.info=NULL, affinity.source=c("reference","local"), NCprobe=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=.7,optical.correct=TRUE,verbose=TRUE,fast=TRUE)
object |
an AffyBatch |
affinity.info |
NULL or an AffyBatch containing the
affinities in the exprs slot. This object can be created
using the function compute.affinities . |
affinity.source |
reference : use the package internal
Non-specific binding data or local : use the experimental
data in object . If local is chosen, either MM probes or a user-defined
list of probes (see NCprobes ) are used to estimate affinities. |
NCprobe |
|
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 |
optical.correct |
Logical value. If TRUE , optical
background correction is performed. |
verbose |
Logical value. If TRUE messages about the progress of
the function is printed. |
fast |
Logical value. If TRUE a faster ad hoc algorithm is
used. |
The returned value is an AffyBatch
object, in which the PM probe intensities
have been background adjusted. The rest is left the same as the
starting AffyBatch
object.
The tunning factor k
will have different meainngs if one uses
the fast (ad hoc) algorithm or the empirical bayes approach. See Wu
et al. (2003)
An AffyBatch
.
Rafeal Irizarry
if(require(affydata) & require(hgu95av2probe) & require(hgu95av2cdf)){ data(Dilution) ai <- compute.affinities(cdfName(Dilution)) Dil.adj<-bg.adjust.gcrma(Dilution,affinity.info=ai,type="affinities") }