Additional file 3.

Table S3. miRNA normalization. Normalization of miRNA expression is challenging and therefore we chose to make 4 different normalizations prior to analysis of differentially expressed miRNAs (PD vs.CR) and compare the results. Normalizes used were mammalian U6 (MammU6) and RNU48 RNAs that is often used as normalizes, miR-193b selected using the Norm Finder program, and finally quintile normalization using the qpcrNorm program (Mar J et al. Data-driven Normalization Strategies for qPCR Data. Technical Report, 2008). The results show a large degree of agreement between normalizations. We argue that the Norm Finder approach is the best normalize approach for our data because quintile normalization is better suited for large gene sets and miRNA-193b is more stable than MammU6) and RNU48 across the samples (data not shown).

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Nordentoft et al. BMC Medical Genomics 2012 5:40   doi:10.1186/1755-8794-5-40