[BioC] Affy miRNA

James W. MacDonald jmacdon at med.umich.edu
Thu Oct 15 20:57:04 CEST 2009

For what it's worth, I just built a cdf and probe package for the Affy 
miRNA chip that will be part of BioC2.5, and which should allow one to 
use the affy pipeline to analyze these data.

That said, I highly doubt the canonical affy analysis (e.g., ReadAffy(), 
rma()) will be a reasonable thing to do, as this chip contains miRNA 
from 71 different species. I would imagine one would want to subset out 
those probesets that pertained to the species at hand before proceeding 
with analysis, and that is a non-trivial exercise.

This post to the BioC listserv by Jenny Drnevich should be quite helpful 
in that endeavor:




Chao-Jen Wong wrote:
> Hi, Lana
> As far as I know, Bioconductor does not have a package for Affy miRNA
> chip yet.   There is a package for Agilent miRNA chips (available from
> BioC 2.5) using rma for normalization.  I would also be interested in
> any suggestions for nomarlization for Affy miRNA chips.
> Thanks,
> Chao-Jen
> Lana Schaffer wrote:
>> Hi,
>> Is there Bioconductor software for the new Affy miRNA chip?
>> Does someone have experience normalizing the Affy miRNA chip?
>> Any suggestions? 
>> Lana Schaffer
>> Biostatistics/Informatics
>> The Scripps Research Institute
>> DNA Array Core Facility
>> La Jolla, CA 92037
>> (858) 784-2263
>> (858) 784-2994
>> schaffer at scripps.edu 
>> _______________________________________________
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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