Error : Results must have the same dimensions
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@phshimaasherif-22566
Last seen 18 months 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

TCGAbiolinks GDC dataset • 240 views
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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

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Hello Tiago,

Thank you for contacting the GDC Help Desk.

For a file like HTSeq Counts, there should only be one aliquot linked. I have created a ticket for this error.

Thank you for catching this error. This fix will hopefully be deployed with our next data release.

Best regards,

Sean Burke, Ph.D. Scientific Support Analyst

Ticket Details --------------------------------- Ticket ID: 12116

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Thank you for illustration.

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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

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