GDCprepare of STAR - counts
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Entering edit mode
mahsa • 0
@422c08cf
Last seen 2.6 years ago
Iran

I want to use GDCprepare for data with STAR - counts workflow in TCGAbiolinks package. It gives me error :

Error in `fn()`:
! Join columns must be present in data.
x Problem with `#gene`.
Run `rlang::last_error()` to see where the error occurred

my function command is :

query <-  GDCquery(
  project = "TCGA-SKCM", 
  data.category = "Transcriptome Profiling", 
  data.type = "Gene Expression Quantification", 
  workflow.type = "STAR - Counts")

GDCdownload(query)
prep <- GDCprepare(query)

the GDCprepare is aborted in the end of the process. I don't know what the problem is. does anyone know ?

GeneExpression TCGAbiolinks • 2.1k views
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Entering edit mode

Please, do you have the latest version 2.25.0 installed?

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

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