GDCprepare of STAR - counts
0
0
Entering edit mode
mahsa • 0
@422c08cf
Last seen 2.7 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 • 2.2k views
ADD COMMENT
0
Entering edit mode

Please, do you have the latest version 2.25.0 installed?

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

BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

ADD REPLY

Login before adding your answer.

Traffic: 451 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6