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GDC server down???

I am trying to use TCGAbiolinks package to analyze illumina methylation array data, but it is saying to me that the server is down, this is happening since last Friday night. Anyone have some information about it??

tcgabiolinks gdc methylation array
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updated by Jade • Jade • written by Gabriel Wajnberg Gabriel Wajnberg

I also have such problem....

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written by Jade • Jade

What exact commands have you both tried? It's possible that the data has just shifted to a new location. The TCGA data is constantly being refined.

Also, which R and package versions?

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written by Kevin Blighe Kevin Blighe

I'm having the same problem (I was using it last week without any problems) My r-base package version is 3.4.4-1xenial0 and TCGAbiolinks version is 2.9.1


#Code:
library(TCGAbiolinks)
query <- GDCquery(project = 'TCGA-LAML',
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type="HTSeq - Counts")

#Error:
Error in value[[3L]](cond) : 
  GDC server down, try to use this package later
• 1 views • link
written by giselesimasrs • giselesimasrs

I report the same:

Error in value[[3L]](cond) : 
  GDC server down, try to use this package later

I will explore further / contact people who may know better.

• 1 views • link
written by Kevin Blighe Kevin Blighe

1 answer

I solved this problem by using devtools::install_github('BioinformaticsFMRP/TCGAbiolinks') to install this package instead of biocLite("TCGAbiolinks"). You can try this way.

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updated by Kevin Blighe Kevin Blighe • written by Jade • Jade

Yes, installing the development version from GitHub also works for me. That's now the second time that a package that interacts with the GDC serves could only function properly after an installation from GitHub. The other was GenomicDataCommons:

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written by Kevin Blighe Kevin Blighe

That worked for me as well. Thanks!

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written by Agata • Agata

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