[BioC] Affy miRNA

Fri Oct 16 12:17:57 CEST 2009

Rao and collaborators have looked at different methods.
A Comparison of Normalization Techniques for MicroRNA Microarray Data
http://www.bepress.com/sagmb/vol7/iss1/art22/

L.

PS: quantile-based normalization is one step in RMA. I am not sure that 
the probe summarization method applies for miRNA (worth a look, but 
those a likely very short - I do not how many probes per miRNA are on 
the affy chip)

Hooiveld, Guido wrote:
> To follow up op on this:
> 
> I also just got the data of my miRNA profiling experiment performed on
> Affy arrays. 
> Upon request Manhong Dai and Fan Meng at the MBNI were so kind to
> 'remap' the miRNA probes last August to mirBASE version 13, both to
> genome loaction and fasta files, for human, mouse and rat. Please find
> the links below. Also note that last september mirBASE updated to
> version 14, so the remapping *might* not completely up to date (although
> I don't think human/mouse/rat are seriously affected).
> 
> With these custom CDF it should be possible to read the data using
> ReadAffy().
> Currently I am evaluating which normalization strategy would be best for
> these relatively small number of probesets. RMA may indeed be an good
> option, but I have read before on this list that VSN may also be a good
> normalization method (in the the discussion regarding the Agilent miRNA
> array [1-color]).
> 
> http://article.gmane.org/gmane.science.biology.informatics.conductor/140
> 96
> 
> 
> Regards,
> Guido
>  
> 
> 
> ------------------------------------------------------------------------
> --------
> From: Manhong Dai
> Sent: Fri 21-8-2009 16:22
> To: Groot, Philip de
> Cc: Hooiveld, Guido; Meng Fan
> Subject: mirbase custom CDF
> 
> 
> Hi,
> 
> 
> mirbase custom CDF is generated.
> 
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.0.
> 0/mirbaseg.asp is based on genome location, the files we used can be got
> by searching 'miRNAgff' in
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.0.
> 0/version.html
> 
> 
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.0.
> 0/mirbasef.asp is based on mirbase fasta files, which are the bottom
> three lines of
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.0.
> 0/version.html
> 
> 
>        
>         Please let me know if you came across any problem.
> 
> 
> Best,
> Manhong
> 
> 
> 
> 
> 
> ------------------------------------------------ 
> Guido Hooiveld, PhD 
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition 
> Wageningen University 
> Biotechnion, Bomenweg 2 
> NL-6703 HD Wageningen 
> the Netherlands 
> tel: (+)31 317 485788 
> fax: (+)31 317 483342 
> internet:   http://nutrigene.4t.com
> email:      guido.hooiveld at wur.nl
> 
> 
> 
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch 
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
>> James W. MacDonald
>> Sent: 15 October 2009 20:57
>> 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.con
>> ductor/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
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>>>>   
>>>
>> --
>> 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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>>
>>
> 
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