[BioC] question about data analysis of Genechip miRNA

[Hooiveld, Guido]

Hi James,

I analyzed my Affymetrix miRNA arrays using a custom, remapped CDF, with the packages 'affy' and 'limma', just like the regular Affymetrix mRNA arrays. Note that this workflow will also do using the default Affy CDF (which is available on BioC). Alternatively, you may want to use the package 'xps'. 
I used quantile normalization because my samples were all from the same tissue that underwent a relatively mild intervention, so I expected most of the miRNAs to remain constantly expressed (in contrast to e.g. comparing different tissues or tumors).

You may want to check these threads for a bit more info on this and related strategies (links point to the starting post of a topic; be sure to click through the complete threads):

http://article.gmane.org/gmane.science.biology.informatics.conductor/31837

http://article.gmane.org/gmane.science.biology.informatics.conductor/29921

http://article.gmane.org/gmane.science.biology.informatics.conductor/32287

http://article.gmane.org/gmane.science.biology.informatics.conductor/24682


Hope this will get you started,
Guido

------------------------------------------------ 
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 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://www.researcherid.com/rid/F-4912-2010


> -----Original Message-----
> From: bioconductor-bounces at r-project.org 
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of 
> James Anderson
> Sent: Tuesday, January 11, 2011 20:14
> To: bioconductor
> Subject: [BioC] question about data analysis of Genechip miRNA
> 
> Hi,
> 
> I need to analyze some Genechip miRNA data in my work, can 
> anybody recommend some packages or methods? or everything is 
> the same as the Affy mRNA Genechip data? 
> 
> Thanks,
> 
> -James
> 
> 
> 
>       
> 	[[alternative HTML version deleted]]
> 
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