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andreamrau / EDGE-in-TCGA

Source code to reproduce results from "Exploring Drivers of Gene Expression in The Cancer Genome Atlas" by Rau et al. (2017)
GNU General Public License v3.0
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Error: Problem connect to Firehose. Please ensure Internet connection is working. #1

Closed NegarMgh closed 2 months ago

NegarMgh commented 2 months ago

Hello, I am not sure if you are still supporting this repository. I have the below problem

rnaseq.ov <- getTCGA(disease="OV", data.type="RNASeq", type="RPKM") Error: Problem connect to Firehose. Please ensure Internet connection is working.

How should I deal with this?

andreamrau commented 2 months ago

Thanks for your question -- there indeed hasn't been much active maintenance on this repo in recent years, and unfortunately I see that the package we used at the time to download the TCGA data (TCGA2STAT) has been archived on CRAN since 2020 (https://cran.r-project.org/web/packages/TCGA2STAT/index.html). Since that package is no longer maintained, that may explain in part the error you're getting.

In any case, I think it would probably now be a better idea to use one of the more recent availale Bioconductor packages to download the TCGA data (e.g., cBioPortalData, TCGAbiolinks, or curatedTCGAdata), from there it should be relatively straightforward to format the data as needed for the rest of the code in this repo or for other analyses.