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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Issue with harmonized data download - please help #243

Open asmagen opened 6 years ago

asmagen commented 6 years ago

Hello,

I get the following error when trying to download the harmonized TCGA data:

> GDCdownload(query)
Downloading data for project TCGA-BRCA
GDCdownload will download....
Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at: 
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
Error in gene.location$ensembl_gene_id : 
  $ operator is invalid for atomic vectors

Any help please?

tiagochst commented 6 years ago

This is when we add ENSEMBL metadata to the SummarizedExperiment object. Problems could be: internet connection, corrupted data downloaded (I recomment deleting the .rda object saved in that case), or maybe an old version of the package. Which are the biomaRt and TCGAbiolinks version you are using?