-
Notifications
You must be signed in to change notification settings - Fork 120
Description
I'm not sure if this is due to a temporary outage with the GDC's servers, but I have been encountering the error "Downloading: 350 MB dcfe1340-4c0a-427c-9fb8-a3cecd8775f0/2ab8eb6b-f68d-4a7a-b9ba-9073633b8d38.methylation_array.sesame.level3betas.txt: Truncated tar archive detected while reading data: Unknown error tar.exe: Error exit delayed from previous errors." when I try downloading DNA methylation data (there seems to be no error when downloading expression data).
These are the commands I've been running:
methylationQuery <- TCGAbiolinks::GDCquery(
project ="TCGA-BRCA",
data.category = "DNA Methylation",
data.type = "Methylation Beta Value",
platform = "Illumina Human Methylation 450"
)
TCGAbiolinks::GDCdownload(
methylationQuery,
directory = "path/on/local/machine"
)
Whereas these worked for expression data:
expressionQuery <- TCGAbiolinks::GDCquery(
project = "TCGA-BRCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts"
)
TCGAbiolinks::GDCdownload(
expressionQuery,
directory = "path/on/local/machine"
)
Thank you for any advice you have with this issue!