How to DESeq2 using miRNA data obtained using TCGAbiolinks
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14 months ago
Mo • 0

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tried to follow many different tutorials but keep getting error messages at different points (possibly because they are out of date tutorials).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

R TCGAbiolinks DESeq2 TCGA • 956 views
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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.

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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?

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14 months ago
Zhenyu Zhang ★ 1.2k

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

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