AffyBatch
into an ExpressionSet
using the robust multi-array average (RMA) expression measure with help of probe sequence.
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, subset=NULL,normalize=TRUE,...)
AffyBatch
NULL
or an AffyBatch
containing the
affinities in the exprs
slot. This object can be created
using the function compute.affinities
.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.NULL
,the MM probes will be used. These probes
are used to estimate parameters of non-specific binding on each
array. These will be also used to estimate probe affinity profiles when
affinity.info is not provided.TRUE
, probe effects in specific binding will
be adjusted.TRUE
, optical
background correction is performed.TRUE
messages about the progress of
the function is printed.TRUE
a faster ad hoc algorithm is
used.ExpressionSet
.
The tuning factor k
will have different meanings if one uses
the fast (add-hoc) algorithm or the empirical Bayes approach. See Wu
et al. (2003)
if(require(affydata) & require(hgu95av2probe) & require(hgu95av2cdf)){
data(Dilution)
ai <- compute.affinities(cdfName(Dilution))
Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities")
}
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