[BioC] Affy miRNA

[cstrato]

Dear Lana,

Maybe you could use package xps, which I have updated to work with 
miRNAs, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-August/029144.html
In case you have a custom CDF for the human miRNAs only you could in 
principle use this CDF file.

Best regards
Christian
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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.
> Lana
>
> ________________________________________
> 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:
>
> http://article.gmane.org/gmane.science.biology.informatics.conductor/19867/match=affybatch+probe
>
> Best,
>
> Jim
>
>
>
> 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
>>> 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
>>>
>>>       
>>     
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>
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>