[BioC] [R] Affy Package

[Uwe Ligges]

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]]
>>
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>