Matching gene-expression data with clinical data: best practices.
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16 months ago

This is a very basic question. I am new to TCGA!

Since I started using TCGA, my approach to downloading gene-expression data is to obtain a manifest file for the gene-expression data I am interested in, and then downloading with the gdc-client.exe data transfer tool.

I have recently started needing clinical data to be part of my analysis. I only know one way to download clinical. What I do is to access TCGA's website, filter in the exploration tab, and click the "clinical" download button. When doing this, I have found no way of matching the clinical data file with the gene expression files, even if I know cases are the same.

One idea I had was to match the clinical/genetic data through the participant barcode. The clinical dataset contains the participant barcode, but the gene-expression files downloaded via manifest do not contain patient barcode. I don't know what to do from there!

In this context, could you recommend best practices for downloading and merging genetic/clinical data through TCGA?

best-practices TCGA • 1.4k views
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After you added your gene expression files to the GDC cart, there are quick download buttons in the cart with which you can download clinical and biospecimen dataenter image description here

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16 months ago
pilargmarch ▴ 110

I really like using the R/Bioconductor package TCGAbiolinks, it gives you clinical and expression data by patient ID.

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16 months ago

Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!

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You can check this

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