[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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