[BioC] Affy miRNA

Thu Oct 15 22:41:13 CEST 2009

All,
Dr. de Groot has given me this link for CDF and annotation files:
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.0.0/mirbaseg.asp 

I would like to note here that Agilent arrays contain >4 arrays on one chip, so the
normalization may not need to be so stringent as with the single Affymetrix arrays.
I have successfully used Agilant-MAD scaled 
normalizeBetweenArrays(x,method="scale")
previously for Agilant data.
Perhaps this will also work for the Affymetrix chips?
Lana

-----Original Message-----
From: Hooiveld, Guido [mailto:Guido.Hooiveld at wur.nl] 
Sent: Thursday, October 15, 2009 1:12 PM
To: James W. MacDonald; Chao-Jen Wong
Cc: Lana Schaffer; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] Affy miRNA

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
> >> 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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> 
> 