Question: GDCprepare stop working for some unknown reason
0
gravatar for ansari.sarabio
18 months ago by
ansari.sarabio0 wrote:

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.

ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 18 months ago by ansari.sarabio0

Cross-posted: https://support.bioconductor.org/p/115959/

ADD REPLYlink written 17 months ago by Kevin Blighe60k
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