Hello,
I would like to get more info, perhaps example calls, on the various
subclasses of ProbeLevelTransform.
I see from a previous post by Mark Robinson, I have the examples:
if(doNorm){
bc <- RmaBackgroundCorrection(cs)
csBC <- process(bc,verbose=verbose,force=force)
setCdf(csBC, cdf)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose,force=force) #time required
setCdf(csN, cdf)
}
What I'd like to be able to do is something akin to what I used to be
able to do with the affy expresso call. That is, specify different
background methods, different normalization methods, such as invariant
set, rma, constant, etc.
I see from the documentation:
Package: aroma.affymetrix
*Class ProbeLevelTransform*
?Object?
?~~|?
?~~+--??AromaTransform?
?~~~~~~~|?
?~~~~~~~+--??Transform?
?~~~~~~~~~~~~|?
?~~~~~~~~~~~~+--?_?ProbeLevelTransform?_
*Directly known subclasses:*
_AbstractProbeSequenceNormalization_,
AllelicCrosstalkCalibration,
_BackgroundCorrection_, BaseCountNormalization,
BasePositionNormalization, DChipQuantileNormalization,
GcRmaBackgroundCorrection, LimmaBackgroundCorrection,
_LinearModelProbeSequenceNormalization_, MatNormalization,
MatSmoothing, NormExpBackgroundCorrection,
OpticalBackgroundCorrection, _ProbeLevelTransform3_,
QuantileNormalization, ReseqCrosstalkCalibration,
RmaBackgroundCorrection, ScaleNormalization, ScaleNormalization3,
SpatialRowColumnNormalization, UnitTypeScaleNormalization
that there are many ProbeLevelTransform subclasses, but I can't seem
to find any examples of how to use them.
If someone could point me in the right direction, I'd be very
grateful.
Thanks very much,
Dick
****************************************************************************
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************
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