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How to use compareCluster for GSEA on the Msigdb database? #653
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Have you seen this information: http://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html#msigdb-analysis ? |
"I have read it. What I mean is using the compareCluster function for analysis, Can the 'fun' parameter accept the value 'GSEA'? I would greatly appreciate your assistance." for example,
thank you |
Yes, that is indeed the way to do it. Note that you can include all arguments that you could set when analyzing a single dataset. Using the included, human example dataset:
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Thank you very much for your help |
Hello,
I am using compareCluster for multi-group GSEA. When using the org.Rn.eg.db database, I set fun=gseGO. If using the Msigdb database, how should I configure it?
Appreciate your help.
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