Differential Expression Analysis for miRNA

Question

[Al]

Hi,

I have miRNA data consists of probes. I am trying to find the differentially expressed genes in one condition vs. another. I am not sure what is the right pipeline. I found more than one probe map to the same gene. I am thinking about getting the average expression for all the probes that map to one gene and assign the average value as the expression to the gene to which these probes are mapped. Then, run limma to find the DEGs. I am not sure if this is the right way or not. Any help would be highly appreciated.

Thank you!

[i.sudbery]

Limma provides the duplicateCorrelation function to deal with cases where you have multiple probes that map to the same gene.