[BioC] Affy miRNA
cstrato at aon.at
Thu Oct 15 22:12:11 CEST 2009
Maybe you could use package xps, which I have updated to work with
In case you have a custom CDF for the human miRNAs only you could in
principle use this CDF file.
e.m.a.i.l: cstrato at aon.at
Lana Schaffer wrote:
> 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.
>> Lana Schaffer wrote:
>>> Is there Bioconductor software for the new Affy miRNA chip?
>>> Does someone have experience normalizing the Affy miRNA chip?
>>> Any suggestions?
>>> Lana Schaffer
>>> 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
>>> Bioconductor at stat.math.ethz.ch
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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