Question: Conduct miRNA (normalized) sequencing using TCGA-PRAD database for survival analysis ?
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gravatar for Björn
10 months ago by
Björn40
Björn40 wrote:

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

ADD COMMENTlink modified 9 months ago by SVV0 • written 10 months ago by Björn40

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

ADD REPLYlink written 10 months ago by Kevin Blighe41k

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by Björn40

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

ADD REPLYlink written 10 months ago by Kevin Blighe41k

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

ADD REPLYlink written 10 months ago by Björn40

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

ADD REPLYlink written 10 months ago by Kevin Blighe41k
0
gravatar for SVV
9 months ago by
SVV0
SVV0 wrote:

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.

ADD COMMENTlink written 9 months ago by SVV0
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