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Question

Problem in downloading data via TCGAbiolinks

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sabarinath.chandrasekharan ▴ 10

@sabarinathchandrasekharan-11149

Last seen 7.5 years ago

Hi ,

I am having trouble downloading data from TCGA. An example output is given below

> library(TCGAbiolinks)

> BRCA_RNASeqV2_version <- TCGAquery_Version(tumor = "brca", platform = "illuminahiseq_rnaseqv2")
Retrieving old version information, please wait...
Error in download.file(url, method = method, ...) : 
  cannot open URL 'http://tcga-data.nci.nih.gov/tcgadccws/GetHTML?query=Archive[revision=10][baseName=*brca*][deployLocation=*illuminahiseq_rnaseqv2*][name=*Level_3*]'

1. Is this because of the recent changes in TCGA? TCGA has posted the following info on their website " 06/10/2016 - Announcement :- As the TCGA DCC contract comes to an end, the TCGA Data Portal and services will be taken offline on July 15th, 2016. ......TCGA data will continue to be hosted at the Genomics Data Commons ( https://gdc.nci.nih.gov/). "

2. Is there a workaround for this problem or should I wait till a patch/update is released by the TCGAbiolinks developers?

Thanks and Regards,

Sab

tcgabiolinks tcgadownload • 4.3k views

ADD COMMENT • link updated 2.9 years ago by H. Z. Amini ▴ 10 • written 7.8 years ago by sabarinath.chandrasekharan ▴ 10

score 0 · Answer 1 · 2016-07-22

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Tiago C. Silva ▴ 270

@tiagochst-7121

Last seen 10 months ago

Miami, US

Hi Sab,

Yes, is this because of the recent changes in TCGA. I rewrote the code do work with GDC. It is already in the github repository, but I still need to update bioconductor repository, which should be done until next week.

This gist has the last version of the code:

By the way, we removed TCGAquery_Version.

Best regards,

Tiago

ADD COMMENT • link 7.7 years ago Tiago C. Silva ▴ 270

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Thank you very much!

ADD REPLY • link 7.7 years ago sabarinath.chandrasekharan ▴ 10

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Hi, I'm going to download the "TCGA-BRCA" with the following command in Rsudio, but I got an error. Would you please help me out ? Thank you!

-------------------------------------Code

query.seq <- GDCquery(project = "TCGA-BRCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", sample.type = c("Primary Tumor","Solid Tissue Normal"), workflow.type = "HTSeq - Counts")

GDCdownload(query.seq)
seq.brca <- GDCprepare(query = query.seq, save = TRUE, save.filename = "brca-RNAseq-Counts.rda", summarizedExperiment = TRUE)

-------------------------------------Error

Error in GDCprepare(query = query.seq, save = TRUE, save.filename = "brca-RNAseq-Counts.rda", : I couldn't find all the files from the query. Please check if the directory parameter is right or GDCdownload downloaded the samples.

ADD REPLY • link 2.9 years ago H. Z. Amini ▴ 10