RNA abundance and DNA copy number are routinely measured in high-throughput
using microarray and next generation sequencing (NGS) technologies, and the
attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized.
We analyzed three biological samples across six miRNA microarray platforms
and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs.
The results were validated for 89 miRNAs by real-time RT-PCR and the use of this assay as a “gold standard” is challenged. Lastly, we implement a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
