[BioC] Affymetrix miRNA array normalization

Wolfgang Huber whuber at embl.de
Fri Jul 16 20:51:29 CEST 2010


Kamila

vsnrma (in the vsn package) might be an option for you to try that 
provides the same probe summary as "normal" rma, but a less aggressive 
between-array normalisation (namely, only a shifting and scaling, i.e. 
affine-linear). See also Deepayan Sarkar et al. in NAR 2009, "Quality 
Assessment and Data Analysis for microRNA Expression Arrays", 
http://nar.oxfordjournals.org/cgi/content/full/37/2/e17

In addition, if you have "negative controls", i.e. probes on the array 
for which you are willing to believe that they most of them don't change 
expression, then you can fit the shifting and scaling factors on these, 
and then apply to all probes.

Best wishes
	Wolfgang

On Jul/11/10 5:11 PM, Steve Shen wrote:
> Will affymetrix qc tool wook?
> http://www.affymetrix.com/estore/partners_programs/programs/developer/tools/devnettools.affx#miRNAQC
>
> steve
>
> On Sat, Jul 10, 2010 at 11:26 AM, Kamila Naxerova
> <naxerova at fas.harvard.edu>wrote:
>
>> Dear list,
>>
>> I was searching the archives for discussions about the Affymetrix miRNA
>> chip... there are only a few threads and most of them  are almost a year
>> old. I was wondering whether in the meantime people had gathered some
>> experience with analysis strategies - normalization in particular - and were
>> willing to share some insights. I do not feel comfortable using RMA because
>> I doubt that total miRNA expression can be assumed to be constant across
>> samples (particularly when studying developmental processes or cancer). Has
>> anybody played with the options?
>>
>> Thanks!
>> Kamila
>>
>>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber



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