[BioC] Affy miRNA
laurent at cbs.dtu.dk
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
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
> 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]).
> From: Manhong Dai
> Sent: Fri 21-8-2009 16:22
> To: Groot, Philip de
> Cc: Hooiveld, Guido; Meng Fan
> Subject: mirbase custom CDF
> mirbase custom CDF is generated.
> 0/mirbaseg.asp is based on genome location, the files we used can be got
> by searching 'miRNAgff' in
> 0/mirbasef.asp is based on mirbase fasta files, which are the bottom
> three lines of
> Please let me know if you came across any problem.
> 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.,
>> 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:
>> 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:
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