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ph.shimaasherif
•
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@phshimaasherif-22566
Last seen 5.0 years ago
Good evening ,
I’m facing a problem in downloading specific data from the GDC website, I’m trying to download the : “TARGET-NBL” RNASeq data , using the TCGAbiolinks package.
I used this command to download the data :
query <- GDCquery (project = "TARGET-NBL",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts")
GDCdownload (query, method = "client", directory = "./Data").
, and I found the following error :
“Error: Results must have the same dimensions”
Please advice. Thank you
Hello,
The problem comes from these two files which are associated with more than one entity ID.
https://portal.gdc.cancer.gov/files/5ad6072e-b35b-4e62-937d-6c7ab706a346 https://portal.gdc.cancer.gov/files/99b36164-ff85-4a6b-85de-77bd42aff592
I need to check with GDC if there is an error in their database or if I need to consider this case. Once I have the answer I'll be able to handle the problem.
It is also weird som cases have two files now: link
Thank you for illustration.
Can I download the other NBL transcriptomic data except the cases associated to these files? As I need it urgently :( If there is any way or other packages to skip these files or overcome this error please advise. Thank you