[BioC] Affymetrix miRNA array normalization

[Thomas Hampton]

Great question. At some point, quantile normalization would not be  
expected to work, because the true
distribution of expression values  under different conditions would  
just be too different.  You'd see
"differential expression" that was an artifact of normalization. I  
have seen RMA cause that with defective arrays.

While I am no expert on all the arguments, I think the proof of the  
pudding is in the verification of
miRNAs your statistical approach found differentially expressed.

Best,

Tom
On Jul 10, 2010, at 11:26 AM, Kamila Naxerova 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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