4-group RNAseq experiment- GSEA vs ssGSEA?
Hi,
I have an RNAseq dataset with 4 treatment conditions. Between those 4 groups, I could establish 3 relevant inter-group comparisons and run classic GSEA or simply score all samples with ssGSEA and run two way ANOVA and correct for multiple testing. Surprisingly, some results I am getting between those two methods are quite different.
What would be a 'more correct' way to tackle this?
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