What is the best pre-processing (background correction + normalization + summarization) algorithm to use in miRNA microarray, using Affymetrix platform?

09 September 2012 1 3K Report

I've heard that RMA might not be applicable and some suggestions would be using VSN (as vsnrma in Bioconductor). Is that right?

Diego Robles Mazzotti

Thank you Edwin. We know that there are several probes in Affymetrix miRNA microarray from other organisms that are not of interest (I'm studying rat). Do you have any insigths if the normalization process is affected when I exclude the non-rat probes before?

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