[BioC] detection calls without MM probes

[Julien Roux]

Hi list,

When using MAS5 detection calls in affymetrix chips, the assumption is 
that the MM probes give a reasonable estimate of background. If we 
normalize affy chips with RMA, MM probes are not used.
In similar way, I was wondering if another method was available to 
estimate the presence/absence of genes without teh use of MM probes?

I think this would be feasible since RMA estimates the parameters of the 
background distribution (bg.parameters), I just don't really know how to 
handle this...
Thanks a lot for your help
Julien

-- 
Julien Roux, PhD student
http://www.unil.ch/dee/page22707.html
Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4221    fax: +41 21 692 4165