Question: help with GDCprepare
gravatar for lawarde.ankita1
2.3 years ago by
lawarde.ankita160 wrote:

Hello Sir/madam,

I'm using GDC data and analyzing the cancer data using TCGAbiolinks package of R. initially I'm following the TCGAbiolinks tutorials ( to get familiar with the workflow. my R version is 3.4.3 and i have updated the Bioconductor too.

But whenever I run the GDCprepare command to prepare the data for further analysis after data downloading it throws following error,

# Query platform Illumina HiSeq with a list of barcode 

query <- GDCquery(project = "TCGA-BRCA",
    data.category = "Gene expression",
                  data.type = "Gene expression quantification",
                  experimental.strategy = "RNA-Seq",
                  platform = "Illumina HiSeq",
                  file.type = "results",
                  barcode = listSamples, 
                  legacy = TRUE)

# Download a list of barcodes with platform IlluminaHiSeq_RNASeqV2


# Prepare expression matrix with geneID in the rows and samples (barcode) in the columns

# rsem.genes.results as values

BRCARnaseqSE <- GDCprepare(query, save = TRUE, 
                           save.filename = "TCGA-BRCA_gene_exp.rda",
                           summarizedExperiment = TRUE)

 |=========================================================================| 100%Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
Error in, y) : 'by' must specify a uniquely valid column

and when i checked the given website, it showed something like this,

  <MartURLLocation database="ensembl_mart_75" default="1" displayName="Ensembl Genes 75" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_75" default="" displayName="Sequence" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_75" default="" displayName="Ontology" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_75" default="" displayName="Genomic features 75" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_75" default="" displayName="Ensembl Variation 75" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="functional_genomics_mart_75" default="" displayName="Ensembl Regulation 75" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="vega_mart_75" default="" displayName="Vega 55" host="" includeDatasets="" martUser="" name="ENSEMBL_MART_VEGA" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="pride_mart_1" default="1" displayName="PRIDE (EBI UK)" host="" includeDatasets="" martUser="" name="pride" path="/pride/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />

I have searched through the similar errors which were regrading the useMart, biomaRt and none were same as this error I'm not able to understand this problem. Please help me with this issue. any suggestions would be very helpful,

Thank you so much.

gdc gdcprepare R tcgabiolinks • 1.3k views
ADD COMMENTlink written 2.3 years ago by lawarde.ankita160

I was able to download and prepare it. Could be the biomart servers were down, so try again?. And if it still isn't working, you could consider downloading the developer version of tcgabiolinks if you haven't done that. Alternatively, it could be due to the fact that you're asking legacy data. Do you really need hg19 data? Otherwise, try leaving legacy=TRUE out?

ADD REPLYlink written 2.3 years ago by mathias.heydt90
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