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Conduct miRNA (normalized) sequencing using TCGA-PRAD database for survival analysis ?

Hi, are there any hands-on tutorials or step-by-step guide to conduct (normalized) miRNA sequencing analysis using TCGA-PRAD database for DE miRNA analysis and survival analysis ? I tried TCGAbiolinksGUI but only with errors. Linkedomics is easy-to-use but lacks enough information on graphs or plots generated which is insufficient for publication

tcga mirna gui linkedomics tcgabiolinksgui
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updated by SVV • SVV • written by Björn • Björn

How comfortable would you feel downloading the raw counts from the GDC Legacy Archive yourself and then re-processing those? Would be invaluable experience.

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written by Kevin Blighe Kevin Blighe

I started it as I don't see other options. Just to save time, I would like to follow tutorials which is easier to follow (for normalized counts/data). TCGAbiolinks vignette is good but has no example on miRNA related to PRAD database.

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written by Björn • Björn

You just need to get the miRNA-seq counts from the GDC Legacy, and then import these into DESeq2 or EDgeR for normalization.

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written by Kevin Blighe Kevin Blighe

Is there advantage in using Harmonized data which is supposed to be corrected for errors?

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written by Björn • Björn

That is the recommendation from the NCBI, i.e., to use the harmonised data

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written by Kevin Blighe Kevin Blighe

1 answer

LinkedOmics data download has normalized data for primary tumor samples. You can check out site http://linkedomics.org/data_download/TCGA-PRAD/. Also data is Normalized RPM and log2.

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written by SVV • SVV

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