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You have two options to explore the GSEA results:
(1) Fetch the p-values and the corresponding gene set statistics and do your own plots. See the output of runEnrichmentAnalysis
(2) We provide two visualisation functions:plotEnrichmentplotEnrichmentDetailed. Please, read the documentation of these functions and let me know if something is not clear.
Thank you for your reply.
But I still don't understand how to extract feature information that can distinguish sample differences,similar to the first principal component.
best,
wang
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