GSEA/ every time using the same input getting slightly different results

Elif

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Mar 1, 2021, 11:25:32 AM3/1/21

to webgestalt

Hello,

I am doing GSEA analysis with using WebGestallt. However, I noticed that when I enter the same rank list, I am always getting slightly different results. Because of that I am not able to exactly reproduce my results. So why it is happening?

And I have several data and I want to compare each GSEA results with each other at the end. If it will create always different results, how I can trust it?

Thank you for your help!

Bests,

Elif

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Mar 1, 2021, 11:56:41 AM3/1/21

to webgestalt

I forgot to mention that all FDR, Enrichment score, NES are changing too.

1 Mart 2021 Pazartesi tarihinde saat 17:25:32 UTC+1 itibarıyla Elif şunları yazdı:

Yuxing Liao

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Mar 1, 2021, 8:30:30 PM3/1/21

to Elif, webgestalt

Because GSEA uses random permutation for significance evaluation. Enrichment score should be the same.

Yuxing

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