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bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
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appropriate background expression ‘universes’ for GSEA #28

Closed Pchaskar closed 11 months ago

Pchaskar commented 1 year ago

I would like to use the GSEA approach on the pre-ranked proteomics data (~ 2000 proteins). I would like to know if I can provide a reference list (appropriate background expression ‘universes’) to the GSEA to estimate the enrichment better. Reference option available in ORA but not GSEA. Thanks

yxngl commented 1 year ago

Hi, that is not possible. For GSEA, you can think the reference is the input space itself.

On Thu, Jun 1, 2023 at 2:37 AM Prasad Chaskar @.***> wrote:

I would like to use the GSEA approach on the pre-ranked proteomics data (~ 2000 proteins). I would like to know if I can provide a reference list (appropriate background expression ‘universes’) to the GSEA to estimate the enrichment better. Reference option available in ORA but not GSEA. Thanks

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