[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
>
>
>         [[alternative HTML version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

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



More information about the Bioconductor mailing list