Has anyone had any experience performing differential expression analysis on miRNA data from Nanostring?

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Mónica Rodrigues

Which kind of analysis did you performed and what do you want to compare? miRNAs gene expression between "normal tissue" and "diseased samples"? In this last case you have to divide one expression value by the other, which will give you a fold change ratio and then you have to define a cut-off, e.g. 2-fold or 3-fold. After that you have to perform Real-Time PCRs to access the expression of your miRNAs of interest.

Hezha Hassan

EdgeR or DESeq2

Anna L Leichter

Thanks, I have nanoString data and approximately 800 miRNAs from a panel examined. Will DESeq be compatible with this type of data? If so I will give it a try!