ssGSEA help (ID: 471802. ssGSEA)

[Vithurran Thavarajah]

Hello,

I'm trying to run an NGS dataset with my own genelist (both .gmt format) but keep running into the following error;

"Error in file(file, "r") : cannot open the connection
Calls: ssGSEA.cmdline
Execution halted"

Not sure if this is an issue with my file formats or a technical issue with the tool?

Kind regards,

Vit

[Ted Liefeld]

Vit

can you provide a job number and we will look into it?

Thanks

Ted

[Ted Liefeld]

NVM Just noticed it was in the title.  From a first guess I think the problem is the quotes that are a part of the input gct file which seems to have been named

"count.gct".gct

Try renaming the file to just count.gct

Hope this helps

Ted

[Vithurran Thavarajah]

Hello Ted, 

I thought the job number was 471802 (in the subject title of previous email). Is this is not, where would I find it please?

On 26 Oct 2022, at 18:42, Ted Liefeld <lie...@broadinstitute.org> wrote:

NVM Just noticed it was in the title.  From a first guess I think the problem is the quotes that are a part of the input gct file which seems to have been named

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[Vithurran Thavarajah]

Apologies Ted, didn't see the follow-up email. I tried re-running (ID: 471814) without any quotation marks and now get a different error;

"Error in rep("null", max.Ng * max.size.G) : invalid 'times' argument

Calls: ssGSEA.cmdline
Execution halted"

[Anthony Castanza]

Hello,

The problem here would appear to be with your gene sets database file. You're specifying it as a gmt file but the file itself is not compliant with the GMT format. Please take a look here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29 correct the file, and give it another go.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Vithurran Thavarajah]

Thanks Anthony and Ted,

Apologies for the late reply. Yes it seems to be a fault on my end with the .gmt file formatting. Seems to work now. Appreciated.

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