I´m just starting to analyze a GeneChip miRNA 2.0 Array dataset, and I just want to know if some one has any experience in its analysis. I was hoping to know which is the best normalization library. I had some experience in the Affy and oligo library, however I´m not clear which is the best option for this microarray. Thanks for your comments.
The easiest way is to use the miRNA QC Tool from Affymetrix, which can be downloaded from their website. It should include annotation files and for normalization RMA is used. I think Affymetrix modified the normalization for the miRNA chip, but I am not sure about that. Check it out yourself, it should be straight forward.
If you want to use R, then e.g. the VSN package could be useful for you (http://bioconductor.org/packages/devel/bioc/html/vsn.html).
These two paper developed their own algorithm and compare it to others:
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