[BioC] expression call

[Jenny Drnevich]

Hi Ido,

The presence/absence calls are calculated from the raw PM and MM probes and 
is done independently from whatever pre-processing suite you decide to use. 
mas5calls() works on an AffyBatch object, so the calls will the same 
regardless of whether you use gcrma(), rma() mas5(), or any combination of 
the options in expresso() to process your probe-level data (AffyBatch 
object) into one value per probeset (exprSet object).

Cheers,
Jenny


>Hi,
>
>how would one get presence or absence calls with gcrma normalized data?
>Is normalizing it with gcrma and then adding the mas5calls the most
>sensible or only way to do it?
>
>Or is there a know cutoff for gcrma normalized data where people
>have measured with RT-PCR that a transcript is actually not expressed?
>
>thank you very much,
>Ido
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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e-mail: drnevich at uiuc.edu