From 971bcb18c30ef246d9e7f4487ae3d85dc0e47d26 Mon Sep 17 00:00:00 2001 From: Benedikt Venn Date: Fri, 16 Dec 2022 13:39:12 +0100 Subject: [PATCH] update gsea docu --- legacy_docs/GSEA.fsx | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/legacy_docs/GSEA.fsx b/legacy_docs/GSEA.fsx index 0e9a0ac6..075fd90c 100644 --- a/legacy_docs/GSEA.fsx +++ b/legacy_docs/GSEA.fsx @@ -35,6 +35,13 @@ For further information visit [GSEA publication](https://academic.oup.com/bioinf ##Method + +Note: There are several methods that are summarized under enrichment analysis. The proposed method makes use of the +hypergeometric distribution. The results are *identical* when using a one sided Fishers' exact test. +Another method is to rank a list of bioitems according to a pvalue or effect size and afterwards test the ranks of +every ontology term using e.g. a Kolmogorov-Smirnov test. The latter version is not covered in this documentation. + + Imagine an experiment, in which 1000 proteins were measured. Within these 1000 proteins there are 25 proteins of a specific functional group (heat shock response). By treating the organism(s) 200 proteins are significantly altered. 10 of the 25 heat responsive proteins