Matching gene-expression data with clinical data: best practices.

Question

[jose.sgomez94]

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?

[Zhenyu Zhang]

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 data

Answer 1

[pilargmarch]

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

Answer 2

[jose.sgomez94]

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

[1769mkc]

You can check this