[BioC] Does hist (affy) function work on probe-pair values or probe-set values?
Jenny Drnevich
drnevich at illinois.edu
Tue Oct 13 16:21:52 CEST 2009
> * 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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>
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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
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu
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