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To run GSEA, your project has to contain at least one categorical factor with exactly two levels (e.g. Treated and Control). If you are running GSEA on RNA-seq data, note that some common normalisation transformations, such as fragments/reads per kilobase of transcript per million mapped reads (FPKM/RPKM) or transcripts per million (TPM) are not considered suitable for GSEA (for more information, please see GSEA documentation). Instead, you should use an approach such as DESeq2 normalisation, trimmed means of M (TMM), or geometric mean.

Running GSEA

To launch GSEA, select the data node with normalised data and then go to Biological interpretation > GSEA (Figure 1).

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