[BioC] Affy miRNA

Lana Schaffer schaffer at scripps.edu
Thu Oct 15 21:08:32 CEST 2009

James and all,
I have asked Affymetrix to create a CDF for the human species on the miRNA chip.
They have created this type of CDF for our custom arrays which we use all the time.

From: James W. MacDonald [jmacdon at med.umich.edu]
Sent: Thursday, October 15, 2009 11:57 AM
To: Chao-Jen Wong
Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Affy miRNA

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
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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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