Re: [R] Affy Package

From: Uwe Ligges <ligges_at_statistik.uni-dortmund.de>
Date: Thu, 27 Dec 2007 11:06:46 +0100

Damn, this was a cross-post (and I replied to all), apologies for my re-cross-posting.

To Roger, the original poster: PLEASE do read the posting guide of R-help before posting and NEVER EVER do crossposting again.

Thanks,
Uwe Ligges

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
>>
>>
>> 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
>>
http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>



R-help_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu 27 Dec 2007 - 10:10:09 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 27 Dec 2007 - 10:30:21 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.