Problems encountered during the survival analysis with TCGA data

Question

[applepie]

Hello Everyone, recently I have been conducting the survival analysis of liver cancer patients expressing CD47, using the TCGA data. The project in this case is "TCGA-LIHC". After downloading the gene expression data of 20 primary tumor sample, I tried to get the counts from the downloaded data. However I have encountered some weird problem:

The R console gave me this output:

One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)

I don't know what's happened... Do anyone know such problem ?

The code I used to generate the data is as follows:

# get gene expression data -----------

# build a query to get gene expression data for entire cohort
query_liver_all = GDCquery(
  project = "TCGA-LIHC",
  data.category = "Transcriptome Profiling", # parameter enforced by GDCquery
  experimental.strategy = "RNA-Seq",
  workflow.type = "STAR - Counts",
  data.type = "Gene Expression Quantification",
  sample.type = "Primary Tumor",
  access = "open")

output_liver <- getResults(query_liver_all)
# get 20 primary tissue sample barcodes
tumor <- output_liver$cases[1:20]
# OR
tumor <- output_liver[output_liver$sample_type == "Primary Tumor", "cases"][1:20]
tumor

# # get gene expression data from 20 primary tumors 
query_liver <- GDCquery(
  project = "TCGA-LIHC",
  data.category = "Transcriptome Profiling", # parameter enforced by GDCquery
  experimental.strategy = "RNA-Seq",
  workflow.type = "STAR - Counts",
  data.type = "Gene Expression Quantification",
  sample.type = c("Primary Tumor", "Solid Tissue Normal"),
  access = "open",
  barcode = tumor)

# download data
GDCdownload(query_liver)

# get counts
tcga_liver_data <- GDCprepare(query_liver, summarizedExperiment = TRUE)

Answer 1

[Zhenyu Zhang]

You should at least put TCGAbiolinks in the title or description.