GDC server down???

Question: GDC server down???

2.7 years ago by

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??

gdc methylation array tcgabiolinks • 3.3k views

ADD COMMENT • link •

modified 2.7 years ago by Jade • 40 • written 2.7 years ago by Gabriel Wajnberg • 70

Not sure what URL TCGAbiolinks uses but the GDC portal is very much up and available here.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by GenoMax ♦ 96k

I also have such problem....

ADD REPLY • link written 2.7 years ago by Jade • 40

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?

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by Kevin Blighe ♦ 70k

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

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by giselesimasrs • 0

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.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by Kevin Blighe ♦ 70k

thanks a lot! Let's see what is going on!

ADD REPLY • link written 2.7 years ago by Gabriel Wajnberg • 70

2.7 years ago by

Jade • 40

Jade • 40 wrote:

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

ADD COMMENT • link modified 2.1 years ago by Kevin Blighe ♦ 70k • written 2.7 years ago by Jade • 40

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:

ADD REPLY • link modified 2.1 years ago • written 2.7 years ago by Kevin Blighe ♦ 70k

Thanks!!!!It worked Fine

ADD REPLY • link written 2.7 years ago by Gabriel Wajnberg • 70

That worked for me as well. Thanks!

ADD REPLY • link written 2.1 years ago by Agata • 0

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