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In Partek Flow, GSEA should be performed on a sample/cell and feature matrix data node, e.g. normalization count data. GSEA is used to detect a gene set/a pathway which is significantly different between two groups. Gene set enrichment should be performed on a filtered gene list; it is used to identify overrepresented gene set/pathway based the filtered gene list using Fisher's exact test. The input data is a filtered list using gene names.
When should I use GSEA or Gene set ANOVA?
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