option to permute by gene_set for calculating FDR?

[Alex Saltzman]

Is there an option to permute by gene_set instead of phenotype? I often have small sample sizes that make phenotype permutation impractical. 

[Alex Saltzman]

Unless you directly permute the gene ranks instead. Apologies if I overlooked it

[Yuxing Liao]

Hi Alex,

I think because we run preranked GSEA. It should permutate by gene set.

Understand and keep in mind the permutation test type.

In GSEAPreranked, permutations are always done by gene set. In standard GSEA you can choose to set  the parameter Permutation type to ‘phenotype’ (the default) or ‘gene set’, but this option is not available in GSEAPreranked.

https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html?_GSEAPreranked_Page

--
You received this message because you are subscribed to the Google Groups "webgestalt" group.
To unsubscribe from this group and stop receiving emails from it, send an email to webgestalt+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/webgestalt/3eafe67a-1ae9-4ff1-94ea-f05ea20b803cn%40googlegroups.com.