Error with TCGA package - TCGAbiolinks
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JAcky • 0
@d6b8183e
Last seen 10 hours ago
Israel

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 for the samples, like tumour purity, LDH levels, and some more wanted features. 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, I'm getting this error and I don't get what is the problem. I tried using metastatic samples instead of primary, and tried without entering the data.type parameter, didn't work. So What does this mean and how do I fix this error? thank you.

> 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)

Note: if there is some other recommended way to download this type of data, using other packages for example, I'll be more than glad to hear. Thanks!

TCGAbiolinks RNASeq CancerData • 262 views
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You can try the Genomic Data Commons Data Portal at

https://portal.gdc.cancer.gov/

or the GenomicDataCommons R/Bioconductor package

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@tiagochst-7121
Last seen 6 days ago
Miami, US

It is working with the github version. Could you update please?

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