Input is not a res or gct file.

[Anindita Bhattacharjee]

Hello Everyone,

I have performed GSEA on my RNA sequencing data and was successful to get the result, however, when I am trying to perform the ssGSEA using same gct file in GenePattern it's showing me the following error:

Error in read.dataset(input.ds) : Input is not a res or gct file.
Calls: ssGSEA.cmdline
Execution halted

I would be very grateful if anyone could assist me with this.

Regards,

Anindita

[Anthony Castanza]

Hi Anindita,

The most common cause of this is a trailing .txt file extension that wasn't removed. If I recall correctly, we put in some protections to the GSEA desktop software has some protections to handle this that are very likely not present in the GenePattern module.
Otherwise, would you be able to provide the job number for the GenePattern module run? We have administrative privileges there and would be able to take a closer look to attempt to figure out what went wrong with the file if you're able to provide the job number.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[Anindita Bhattacharjee]

Please find the attached screenshot. Is this what you are looking for?

--
You received this message because you are subscribed to a topic in the Google Groups "gsea-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/gsea-help/z6Kzb7L7snI/unsubscribe.
To unsubscribe from this group and all its topics, send an email to gsea-help+...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/gsea-help/a69fa1b2-4f8e-4fe3-8209-23686309604en%40googlegroups.com.

[Anthony Castanza]

Hi Anindita,

Yes, thanks for providing this.
Looking at the job data, it does appear to be the file extension issue. You may need to enable "show hidden file extensions" or similar in your operating system, and then remove the extra .txt extension that the GenePattern module isn't compensating for.
Once you do this, and supply the corrected file the job should run. If, at that point, it still doesn't, please let me know.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

[Anindita Bhattacharjee]

Hi Anthony,

Thank you for your help, I successfully ran the ssGSEA pipeline. Could you guide me on how to visualize and interpret the ssGSEA results?

Regards,

Anindita

To view this discussion visit https://groups.google.com/d/msgid/gsea-help/1f6e9f29-92e9-492f-8a99-92ee460735e4n%40googlegroups.com.

[Anthony Castanza]

Hi Anindita,

It depends on what you're trying to do. A common thing to do is to run hierarchical clustering and visualize the heat map, but we also offer tools like ssGSEA.ROC that do some comparative analysis of you have two phenotypes in your data.

I don't know enough about your experiments to give specific advice, sorry!

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

To view this discussion visit https://groups.google.com/d/msgid/gsea-help/CACZO09DLToTAi5JrTGeEMoQeioD5h4wdUC9wquzZp2GYVhsX7w%40mail.gmail.com.

[Anindita Bhattacharjee]

Yes, I did the heatmap and performed a ssGSEA.ROC is showing some error. I have attached the error text.

Job ID: 

684627. ssGSEA.ROC

To view this discussion visit https://groups.google.com/d/msgid/gsea-help/CAGCeyZzLe-b_YCzihB78f6ET5nrEgM8LXiUhNM6NtM0b_D3Yqg%40mail.gmail.com.

[Anthony Castanza]

Hi Anindita,

It looks like there are some non-standard gene set names that might be causing issues. The standard convention for set names strips parenthesis and doesn't have trailing underscores. Something about this seems to be causing issues with ssGSEA.ROC. I did a test run stripping these out from the set names just using text editor, and it seems to have completed successfully.
Let me know if you try this and it still has issues.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego