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

Question

[Björn]

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

[Kevin Blighe]

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

[Björn]

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.

[Kevin Blighe]

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

[Björn]

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

[Kevin Blighe]

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

Answer 1

[SVV]

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.