[BioC] miRNA normalization using affy package?

Hooiveld, Guido Guido.Hooiveld at wur.nl
Sat Nov 6 09:12:07 CET 2010

Hi Michal,

I also performed a miRNA profiling study using the Affymetrix miRNA arrays. 
Manhong Dai and Fan Meng were so kind to remap all probes back to the mirBASE information for human, mouse and rat, both to genome location and fasta files. I used their CDF (v13) instead of the default one Affy provides. The CDF version 13 was generated using info from mirBASE v15. Note that early September mirBASE was updated to version 16, so the remapping *might* not completely up to date (although I don't think human/mouse/rat are seriously affected).

With these custom CDF (but also the Affy's default one) it should be possible to read the data using ReadAffy().
I have used RMA for normalization, 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]).

This paper may also be of interest regarding normalization strategies of miRNA arrays in general:


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 
> Michal Blazejczyk
> Sent: Friday, November 05, 2010 15:11
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] miRNA normalization using affy package?
> Hi everyone,
> I'm curious to hear what R packages you would recommend for 
> the normalization of data from Affymetrix miRNA arrays?
> Is the standard affy package performing well?
> What CDF package is best to use?
> Best regards,
> Michal Blazejczyk
> FlexArray Lead Developer
> McGill University and Genome Quebec Innovation Centre
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