giving weight to DEG from limma output
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@shamim-sarhadi-9395
Last seen 7.6 years ago

Hi

I have DEG result from limma,now I want to analysis GSEA with "enrichr" service  http://amp.pharm.mssm.edu/Enrichr/ ,but it asks me for a weight per gene between 0-1 for a high resolution results, dose anyone have any ideas?

limma GSEA • 949 views
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Aaron Lun ★ 28k
@alun
Last seen 1 hour ago
The city by the bay

You'd be better off asking the Enrichr authors for what the weights should be. Different methods use weights in different ways, so there isn't any one-size-fits-all definition that can be used to answer your question. More generally, if you're just doing gene set testing, you might consider methods like goana and kegga that are already available in limma.

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Thank you Aaron lun ,I think kegga in limma is a better choice

 

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