GDCprepare stop working for some unknown reason
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Entering edit mode
2.7 years ago

Dear all,

I am working with TCGAbiolinks for a while. It was working smoothly until now. I'd like to change some setting of the script and for an unknown reason it stops working. It asked me to start over and after it can not prepare data by GDprepare function. I get this error:

Error in if (any(duplicated(query$results[[1]]$cases)) & query$data.type !=  : 
  argument is of length zero

This is my script:

#GDCquery: Searching GDC data for download
##downloading and prepare
query <- TCGAbiolinks::GDCquery(project= c("TCGA-STAD"),
                                data.category = "Transcriptome Profiling",
                                data.type = "Gene Expression Quantification",
                                workflow.type = "HTSeq - Counts",
                                file.type = "htseq.counts.gz",
                                sample.type = c("Primary solid Tumor", "Metastatic" , "Solid Tissue Normal"),
                                experimental.strategy = "RNA-Seq")
query <- TCGAbiolinks::GDCdownload(query)
library("SummarizedExperiment")
data <- TCGAbiolinks::GDCprepare(query , 
                                 save = TRUE , 
                                 save.filename = "STADesxp.rda" , 
                                 directory = "GDCdata" , 
                                 summarizedExperiment = TRUE , 
                                 remove.files.prepared = FALSE)

Thank you very much in advance!

Sara A.

tcgabiolinks GDCprepare RNA-Seq • 1.6k views
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