[R] Affy Package

[Uwe Ligges]

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
> 
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