[R] Affy Package
ligges at statistik.uni-dortmund.de
Thu Dec 27 11:06:46 CET 2007
Damn, this was a cross-post (and I replied to all), apologies for my
To Roger, the original poster: PLEASE do read the posting guide of
R-help before posting and NEVER EVER do crossposting again.
Uwe Ligges wrote:
> Vallejo, Roger wrote:
>> Dear R Users,
>> In the expresso function, which combination of these methods for data
>> pre-processing (when using affymetrix oligo arrays) is the best:
>> bgcorrect.metod = rma rma2 mas
>> normalize.method = qspline quantiles loess
>> pmcorrect.method = pmonly subtractmm mas
>> summary.method = liwong avgdiff medianpolish mas
>> There are many options within each method. I would appreciate a hint
>> on the best combination.
> There is more than one implemented, hence we can guess that there is no
> generally best one among these, i.e. it depends on your data what to use.
> Uwe Ligges
>> Thank you very much in advance.
>> Roger L. Vallejo, Ph.D.
>> Computational Biologist & Geneticist
>> U.S. Department of Agriculture, ARS
>> National Center for Cool & Cold Water Aquaculture
>> 11861 Leetown Road
>> Kearneysville, WV 25430
>> Voice: (304) 724-8340 Ext. 2141
>> Email: roger.vallejo at ars.usda.gov
>> [[alternative HTML version deleted]]
>> R-help at r-project.org mailing list
>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
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