[BioC] Does hist (affy) function work on probe-pair values or probe-set values?

[Jenny Drnevich]

>     * The hist function builds the density graph using the probe pair
>       values when an Affybatch object is used (that is, raw data).
>     * The hist function builds the density graph using the probe set
>       values when an expression set object is used (that is, after
>       preprocessing).
>
>Is that correct?

Yes. The Affybatch object only has probe-level data in it, so that is 
what is used for the density graph. You can only get probe set data 
after applying some algorithm to the probe-level data, and an 
ExpressionSet object contains only the probe set data.

Cheers,
Jenny


>Thanks in advance,
>Javier
>
>
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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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