| expressopdnn {affypdnn} | R Documentation |
a wrapper to perform the PDNN method.
pdnn.scalevalue.exprSet(eset, scale.to=500)
expressopdnn(abatch,
# background correction
bg.correct = FALSE,
bgcorrect.method = NULL,
bgcorrect.param = list(),
# normalize
normalize = FALSE,
normalize.method = NULL,
normalize.param = list(),
pmcorrect.method = c("pdnn", "pdnnpredict"),
# pdnn
findparams.param = list(),
# expression values
summary.subset = NULL,
# PDNN expression values scaling
eset.normalize = TRUE,
scale.to = 500,
# misc.
verbose = TRUE,
widget = FALSE)
abatch |
object of AffyBatch-class |
bg.correct |
a boolean to express whether background correction is wanted or not. |
bgcorrect.method |
the name of the background adjustment method |
bgcorrect.param |
a list of parameters for bgcorrect.method (if needed/wanted) |
eset |
An object of exprSet-class |
normalize |
normalization step wished or not. |
normalize.method |
the normalization method to use |
normalize.param |
a list of parameters to be passed to the normalization method (if wanted). |
pmcorrect.method |
the name of the PM adjustement method (only two choices here, default to 'pdnn'). |
findparams.param |
a list of parameters to be passed to find.params.pdnn |
eset.normalize |
is any normalization step on expression values to be performed |
scale.to |
a value to scale against. |
summary.subset |
a list of 'affyids'. If NULL, a
expression summary value is computed for everything on the chip. |
verbose |
logical value. If TRUE it writes out some
messages. |
widget |
a boolean to specify the use of widgets (the package tkWidget is required). NOTE: this not yet implemented ! |
expressopdnn is very similar to expresso. It is
mainly a wrapper around the pre-processing steps `background
correction', `normalization', `perfect match correction' and
the PDNN method to compute expression values (see the first
reference for more details about the preprocessing steps and
and the second reference for further details about the PDNN method).
The wrapper expresso has no way to handle easily the
computation of chip-wide results that have to be used during
the computeExprSet step. An easy way to overcome this
was to write this simple wrapper.
pdnn.scalevalue is performed after the expression values
have computed to somehow `normalize' the values between different
chips. When setting normalize to TRUE this step
might be considered unnecessary (and the eset.normalize set
to FALSE).
An object of exprsSet-class, with an attribute
pps.warnings as returned by the method computeExprSet.
expresso and \code{computeExprVal.method.pdnn}
## load pre-computed parameters
data(hgu95av2.pdnn.params)
library(affydata)
data(Dilution)
## one CEL to go faster
afbatch <- Dilution[, 1]
## Take only few IDs (the 10 first)
ids <- ls(getCdfInfo(afbatch))[1:10]
eset <- expressopdnn(afbatch, bg.correct=FALSE,
normalize=FALSE,
findparams.param=list(params.chiptype=hgu95av2.pdnn.params,
give.warnings=FALSE),
summary.subset=ids)