User: jshelton

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jshelton0
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Posts by jshelton

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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... Here is my session info: > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X El Capitan 10.11.6 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphic ...
written 3.0 years ago by jshelton0
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Answer: A: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... Thanks, I rebuilt everything (from R up). I can get most of this to work but now I get: > cnv <- TCGAbiolinks::getGistic("HNSC")​ Error: 'getGistic' is not an exported object from 'namespace:TCGAbiolinks'​ Any suggestions:) ...
written 3.0 years ago by jshelton0
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... Okay so I spoke too soon. The script is now stalling at a later step. Now when I run the next steps I get : > GDCdownload(query.exp) Of the 82 files for download 2 already exist. We will download only those that are missing ones. GDCdownload will download 80 files. A total of 121.269906 MB Dow ...
written 3.0 years ago by jshelton0
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... I just tried the same script again today and it worked. There server issue may have cleared up? Thanks for your help ...
written 3.0 years ago by jshelton0
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Comment: C: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... I have TCGAbiolinks_2.3.4 Thanks ...
written 3.0 years ago by jshelton0
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Answer: A: TCGAbiolinks GDCquery downloads a file that reads "message": "internal server er
... So my actual gene list and sample list is longer (I can email you it if you would like but it is in the sam format as my posted code). From the download I get: > query.exp <- GDCquery(project = "TCGA-HNSC", + legacy = TRUE, + data.category = "Gene ...
written 3.0 years ago by jshelton0
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TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"
... Hi, I am attempting to download data but instead get a file with the extension '.tar.gz'. However, this is not a compressed file. It is a text file with the words: {   "message": "internal server error" } Below is the code I ran: samples <- c("TCGA-BA-4074", "TCGA-BA-4075") interesting.gene ...
tcgabiolinks gdc written 3.0 years ago by jshelton0

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For TCGAbiolinks GDCquery downloads a file that reads "message": "internal server error"

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