Retrieve TCGA file ID and associated barcode with TCGAbiolinks: "GDC server down"

Question

[user31888]

I am trying to follow the example here to get file names and associated barcodes using TCGAbiolinks.

> library(TCGAbiolinks)
> query <- GDCquery(project = c("TCGA-BRCA"),
              data.category = "Raw Sequencing Data",  
              sample.type = "Primary solid Tumor")
Error in value[[3L]](cond) :
  GDC server down, try to use this package later

I checked the status of the server but apparently it is ok:

> library(GenomicDataCommons)
> status()
$commit
[1] "e9e20d6f97f2bf6dd3b3261e36ead57c56a4c7cc"

$data_release
[1] "Data Release 12.0 - June 13, 2018"

$status
[1] "OK"

$tag
[1] "1.14.1"

$version
[1] 1

Is it possible to similarly get the file names and corresponding barcodes using GenomicDataCommons, which seems to work better?

[1830416019]

Sir, I have downloaded the gitub version of TCGAbiolinks package, but the problem is still not solved.

[Kevin Blighe]

Hello, what is the error message? Which lines of code are you running?

[1830416019]

query <- GDCquery(project = "TCGA-READ", + experimental.strategy = "RNA-Seq", + data.category = "Transcriptome Profiling", + data.type = "Gene Expression Quantification", + workflow.type = "HTSeq - FPKM") Error in value[3L] : GDC server down, try to use this package later

[1830416019]

Dear Mr. Kevin Blighe, I am currently using the package TCGabiolinks to download colorectal cancer data. I have reinstalled the GitHub version of the package according to what you mentioned before, but I still haven't solved the problem. Is there any other method?thank you！！

code: query <- GDCquery(project = "TCGA-READ", + experimental.strategy = "RNA-Seq", + data.category = "Transcriptome Profiling", + data.type = "Gene Expression Quantification", + workflow.type = "HTSeq - FPKM")

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

[GenoMax]

GDC server down, try to use this package later

Looks like either GDC server is down or you are not able to reach it from your local computer (you will have to check on local firewall restrictions).

Answer 1

[Kevin Blighe]

Hello,

Please install the GitHub version by doing the following:

require(devtools)
install_github("BioinformaticsFMRP/TCGAbiolinks")

Then it should work.

query <- GDCquery(project = c("TCGA-BRCA"),
+               data.category = "Raw Sequencing Data",  
+               sample.type = "Primary solid Tumor")
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
--------------------
oo Filtering results
--------------------
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------

Kevin

[user31888]

Works ! However, it cannot find function datatable in the second part of the code.

> datatable(getResults(query, rows = 1:100,cols = c("file_name","cases")), 
              filter = 'top',
              options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
              rownames = FALSE)
Error in datatable(getResults(query, rows = 1:100, cols = c("file_name",  :
  could not find function "datatable"

[user31888]

My mistake. I just had to get rid of the datatable from the DT package (cannot open browser on the server I use anyway).

[Kevin Blighe]

Great! - all good now?