About selection of samples in TCGA

Question

[luciano.anselmino]

Good day to all, I'm trying to download RNA-seq data from the TCGA database. I need to select a group of recurrent colon cancer samples, the information on whether the cancer was recurrent or not is in the metadata. I have not found a way to filter the samples by matadates to stay with the ones that interest me. Does anyone have an idea of whether it is possible to do this, or should I see one by one? Thank you.

Answer 1

[sophiespo]

It might be useful for you to look at the R package TCGA Biolinks (http://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html ). It has help information for downloading the clinical information. You could parse the clinical data for the recurrent samples in R, and then you could just download the appropriate samples.

[Kevin Blighe]

Hey sophiespo, you may want to check the link that you posted. You have to add a space before the final parenthesis (bug in Biostars system)

[sophiespo]

Thanks! I didn't know that. I've updated the link.