How to DESeq2 using miRNA data obtained using TCGAbiolinks

Question

[Mo]

Hi,

I'm sorry if this is a bit of a stupid question, I am currently trying to obtain miRNA expression data from TCGA-COAD using TCGAbiolinks to carry out miRNA differential expression analysis between normal and tumour samples using DESeq2. I have tried to follow many different tutorials but keep getting error messages at different points (possibly because they are out of date tutorials). Can anyone guide me to a solid tutorial they would recommend or give me a helping hand.

Thanks in advance

[ATpoint]

Show your code on how you get the data. Once you have a gene by sample matrix of raw counts just read the DESeq2 manual.

[swbarnes2]

miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to get is valid for miRNA analysis?

Answer 1

[Zhenyu Zhang]

before you start, where will your normals come from? TCGA doesn't have them in general (except very few cases)