giving weight to DEG from limma output
1
0
Entering edit mode
@shamim-sarhadi-9395
Last seen 7.3 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 • 903 views
ADD COMMENT
1
Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 7 hours 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.

ADD COMMENT
0
Entering edit mode

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

 

ADD REPLY

Login before adding your answer.

Traffic: 1135 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6