[BioC] affy Package

Naomi Altman naomi at stat.psu.edu
Sat Dec 29 17:34:12 CET 2007

Hi Roger,

If you do not use a standard set of methods (e.g. rma or gcrma) then 
you will need to justify your choice to your publication 
audience.  So, I do not use these primary methods unless I have a 
compelling reason to do so.


At 05:55 PM 12/26/2007, 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.
>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]]
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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