Error with TCGA package - TCGAbiolinks
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7 weeks ago
JACKY ▴ 10

I'm trying to download SKCM melanoma samples to R, using the package TCGAbiolinks. The wanted data is RNA-seq expression matrix, along with the metadata. Pretty basic.

This is the code right from the beginning:

library(TCGAbiolinks)
GDCprojects = getGDCprojects()
TCGAbiolinks:::getProjectSummary("TCGA-SKCM")

query_TCGA = GDCquery(
  project = "TCGA-SKCM",
  data.category  = "Transcriptome Profiling", 
  data.type = "Gene Expression Quantification",
  experimental.strategy = "RNA-Seq",
  workflow.type = "STAR - Counts",
  sample.type = c("Primary Tumor")) # picked primary
skcm_res = getResults(query_TCGA) # make results as table

GDCdownload(query = query_TCGA)
tcga_data = GDCprepare(query_TCGA)

However, the last line of code gives me this error:

> tcga_data = GDCprepare(query_TCGA)
|=================================================================================|100%                      Completed after 24 s 
Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
ℹ Locations 2, 3, and 4 don't exist.
ℹ There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

What does this mean and how do I fix this error? thank you.

TCGA r cancer • 316 views
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Please post on Bioconductor Support: https://support.bioconductor.org/

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Thank you Kevin Blighe

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