How I can process miRNA-seq TCGA data to quantificate miRNA expression?

Alan Jhones Barbosa de Assis @Alan_Barbosa_De_Assis

07 July 2019 1 2K Report

I have downloaded the miRNA-seq data for pancreatic cancer from TCGA. Now, I would like to see the expression of a particular miRNA across all the samples - or at least to classify samples into two groups: high and low expression. What exactly should I do?

Yuan-Bo Pan

Did You download the counts data (level 3 data) for the miRNA-seq?

You should use the R package "DESeq2" or "edgER" to normalize the counts data and then divide all samples into high And low expression groups according to the median expression level of the specifc gene.

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