Hello,

I am trying to download and prepare RNA-seq data from the TCGA-LAML project using the TCGAbiolinks package in R. The GDCquery and GDCdownload steps work, but GDCprepare fails with an error about a missing disease_response column.

The code I ran:

library(TCGAbiolinks)

query <- GDCquery(project = "TCGA-LAML",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type = "STAR - Counts",
                  experimental.strategy = "RNA-Seq")

GDCdownload(query)

Data <- GDCprepare(query, summarizedExperiment = TRUE) # Error occurs here

The full error message:

Starting to add information to samples

 => Add clinical information to samples

Error in `dplyr::select()`:

! Can't select columns that don't exist.
 Column `disease_response` doesn't exist.

Run `rlang::last_trace()` to see where the error occurred.

My environment:

R version: 4.5.1 (2025-06-13 ucrt)

TCGAbiolinks version: 2.39.0 (manually installed from the .zip)

Operating System: Windows 10 x64 (build 19045)

What I have already tried:

I first encountered this with version 2.38.0.

I updated to version 2.39.0 by manually installing the .zip, but the error persists.

I confirmed that the clinical data for TCGA-LAML from the GDC portal does not contain a disease_response column.

It seems the package's internal function is looking for a clinical column that is no longer provided by the GDC. How can I resolve this?

Thank you for any help.