Cannot connect to Firehose Internet

thesimranvenkat commented 1 year ago

I can't seem to load the data in the TCGA_preprocessing script line:

for (cancer_type in all_cancers) {
  print(paste0("Processing cancer ", cancer_type))
  mtx <- load_data(disease = cancer_type, data.type = data.type, type = type, data_dir = data_dir, force_reload = FALSE)
  # Prepare expression data
  expr <- mtx$merged.dat[ , 4:ncol(mtx$merged.dat)] %>% as.matrix
  cancer_counts <- rbind(cancer_counts, c(cancer_type, nrow(expr)))
}  

Error: Problem connect to Firehose. Please ensure Internet connection is working.

Error in gzfile(file, "wb") : cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
  cannot open compressed file 'D:/Bioinformatics/data/mtx_ACC_RNASeq2_.rda', probable reason 'No such file or directory'

I'm currently running this on R.4.0.2 on a windows system and have no options to switch over to another OS at the moment.

mdozmorov commented 1 year ago

Hi @thesimranvenkat, the Firehose has been decommissioned. As well as the TCGA2STAT package. The error is the same on my end, if I try to redownload (force = TRUE) the data. I would recommend the curatedTCGAData and TCGAutils packages.

If you would still like to use my scripts, I uploaded the data I have downloaded previously here. You need to download it on your computer and adjust the data_dir variable.

thesimranvenkat commented 1 year ago

Thank you so much for this. Just wanted to confirm, despite TCGA2STAT being decommissioned, the survival related scripts would still work? I can still run the Analysis 2 chunk?

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From: Mikhail Dozmorov @.> Sent: Friday, March 31, 2023, 7:15 PM To: mdozmorov/TCGAsurvival @.> Cc: thesimranvenkat @.>; Mention @.> Subject: Re: [mdozmorov/TCGAsurvival] Cannot connect to Firehose Internet (Issue #16)

Hi @thesimranvenkathttps://github.com/thesimranvenkat, the Firehose has been decommissioned. As well as the TCGA2STAT package. The error is the same on my end, if I try to redownload (force = TRUE) the data. I would recommend the curatedTCGADatahttps://bioconductor.org/packages/curatedTCGAData/ and TCGAutilshttps://bioconductor.org/packages/TCGAutils/ packages.

If you would still like to use my scripts, I uploaded the data I have downloaded previously herehttps://drive.google.com/drive/folders/1rUpbpXtvglUzgXGzzCMAvt8C0Wp3ntCp?usp=share_link. You need to download it on your computer and adjust the data_dir variable.

— Reply to this email directly, view it on GitHubhttps://github.com/mdozmorov/TCGAsurvival/issues/16#issuecomment-1491839586, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATBCQJXR5ORZBVJ7XIVUBLTW63DG3ANCNFSM6AAAAAAWOFXE4M. You are receiving this because you were mentioned.Message ID: @.***>

mdozmorov commented 1 year ago

Yes, all analyses should work and be accurate.

mdozmorov / TCGAsurvival

Cannot connect to Firehose Internet #16