GSEA analysis not possible error subgroup 1 has no samples

Rademaker Gilles

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Jul 26, 2023, 8:47:16 PM7/26/23

to UCSC Xena and Cancer Genomics Browser

Hi,

Everytime I try to do a GSEA analysis I got this error message appearing. I always have samples in both group and don't really know what to do. Could you please give me an idea?

Thanks,

Gilles

Mary Goldman

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Jul 26, 2023, 8:55:41 PM7/26/23

to Rademaker Gilles, UCSC Xena and Cancer Genomics Browser

Hi Gilles,

We believe you are seeing the issue we just discovered where if you make subgroups but do not rename the individual subgroups, GSEA will give the error you mentioned. We are looking into a fix but in the meantime please rename both of your subgroups to anything besides the default. More information on how to do this can be found here: https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-2#video-of-steps-2-4

If this does not fix the issue, please create a bookmark of your current display and send it to us so we can investigate further: https://ucsc-xena.gitbook.io/project/overview-of-features/bookmarks

Best,

Mary

-----

Mary Goldman (she/her), Design and Outreach Engineer

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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Rademaker Gilles

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Jul 27, 2023, 10:56:48 AM7/27/23

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It works. Thank you very much!!

Mary Goldman

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Aug 7, 2023, 5:24:36 PM8/7/23

to Rademaker Gilles, UCSC Xena and Cancer Genomics Browser

HI Gilles,

I wanted to let you know that this has been fixed. You should no longer need to change your subgroup names in order to run a GSEA. If you run into any other issues, please let us know.

Best,

Mary

-----

Mary Goldman (she/her), Design and Outreach Engineer

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

To view this discussion on the web visit https://groups.google.com/d/msgid/ucsc-cancer-genomics-browser/0aa1e9a2-f25c-40e7-86f8-2d8a1d33be59n%40googlegroups.com.

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