[R] Affy Package

From: Vallejo, Roger <Roger.Vallejo_at_ARS.USDA.GOV>
Date: Mon, 24 Dec 2007 15:56:24 -0500


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

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