Hi,

I am trying to work with TCGAbiolinks, but am having problem with GDCprepare. It fails to connect to BioMart web service. 

​queryGBM <- GDCquery(project = "TCGA-GBM",
+                   data.category = "Gene expression",
+                   data.type = "Gene expression quantification",
+                   platform = "Illumina HiSeq", file.type  = "normalized_results",
+                   experimental.strategy = "RNA-Seq",
+                   barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
+                   legacy = TRUE)
Accessing GDC. This might take a while...
> GDCdownload(queryGBM)
All samples have been already downloded
> data <- GDCprepare(queryGBM)
  |============================================================================================| 100%
Downloading genome information. Using: Homo sapiens genes (GRCh37.p13)
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

But I am able access the BioMart web service from biomart 

>entrez=c("673","837")
> goids = getBM(attributes=c('entrezgene','go_id'), filters='entrezgene', values=entrez, mart=ensembl)
> head(goids)
  entrezgene      go_id
1        673           
2        673 GO:0005737
3        673 GO:0005886
4        673 GO:0005634
5        673 GO:0005829
6        673 GO:0005509

What could be the issue?

Thanks and Regards,

Sabari

Hi,

As you used legacy = TRUE, TCGAbiolinks will access Ensembl75 (hg19/GRCh37) . One of this servers might have been temporarily down.

Ensembl75 can be accessed with one of these codes (source: https://www.biostars.org/p/136775/):

grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

or 

ensembl_75 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="feb2014.archive.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

These sources are used in TCGAbiolinks for Ensembl75 (hg19/GRCh37).

https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/0fa5099c1c9d0d1bdab9365146e769af72c7c54e/R/TCGAPrepare.R#L502-L531

GDCprepare throwed a different error when I tried with a different data set

> query <- GDCquery(project = "TCGA-LUSC", data.category = "Gene expression", data.type = "Gene Expression Quantification", platform = "Illumina HiSeq", file.type  = "normalized_results", experimental.strategy = "RNA-Seq", sample.type = c("Primary solid Tumor"),  barcode = c("TCGA-85-8481-01A-11R-2326-07"," TCGA-56-8626-01A-11R-2403-07 "), legacy = TRUE)
Accessing GDC. This might take a while...

> GDCdownload(query)
All samples have been already downloded

> data <- GDCprepare(query)
Error in names(frame)[names(frame) == "x"] <- name : 
  names() applied to a non-vector

> data <- GDCprepare(query)

> data
function (..., list = character(), package = NULL, lib.loc = NULL, 
    verbose = getOption("verbose"), envir = .GlobalEnv) 
{
    fileExt <- function(x) {
        db <- grepl("\\.[^.]+\\.(gz|bz2|xz)$", x)
        ans <- sub(".*\\.", "", x)
        ans[db] <- sub(".*\\.([^.]+\\.)(gz|bz2|xz)$", "\\1\\2", 
            x[db])
        ans
    }
........................
    REST OF THE CODE HERE , REMOVED DUE TO WORD COUNT CONSTRAINT IN POSTING
........................
                  }
                  if (found) 
                    break
                }
                if (verbose) 
                  message(if (!found) 
                    "*NOT* ", "found", domain = NA)
            }
            if (found) 
                break
        }
        if (!found) 
            warning(gettextf("data set %s not found", sQuote(name)), 
                domain = NA)
    }
    invisible(names)
}
<bytecode: 0x0000000012c81af0>
<environment: namespace:utils>
> 

Is this a problem with accessing the API or is there any problem with my query structure?

Thanks,

Sabari

I am still having this problem of GDCprepare not being able to connecto Biomart server, while other programs can. anybody else is facing this problem? Is there any work around?