[BioC] normalize AffyBatch object by control spots? - SOLVED, partially

[Jenny Drnevich]

OK, I should have kept looking a little more before I sent out this 
message. It appears that the normalize.AffyBatch.loess() method can accept 
a subset of the data. Has anyone used this method successfully? I'm not 
sure how the subset of probes should be indicated - perhaps by their row 
numbers from exprs(affybatchobject)?

Jenny


At 01:56 PM 9/27/2006, Jenny Drnevich wrote:
>Hi all,
>
>Does anyone know of an existing function in any package to normalize an
>AffyBatch object using a set of control probesets only? I've looked through
>the functions in the affy package and searched the archives, but couldn't
>find anything. There is an option similar to what I want in the
>normalizeWithinArrays(method="control") function in limma, but I wanted to
>find out if I had missed something before trying to write my own function.
>
>Thanks,
>Jenny
>
>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 uiuc.edu
>
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