[BioC] [R] Affy Package

[Robert Gentleman]

Hi,
   Please do not cross-post. Pick one list and post to it. Please spell 
and capitalize correctly: it is the affy package, not Affy,

  and perhaps the best answer to your question can be found at:

  http://affycomp.biostat.jhsph.edu/

  and in particular "best" is not a well defined concept, it depends on 
what you want to achieve.

  best wishes
    Robert


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
>  
>  
> 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]]
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org