[BioC] Affymetrix miRNA array normalization

Kamila Naxerova naxerova at fas.harvard.edu
Sat Jul 10 17:26:43 CEST 2010


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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