Run GSEA on pre-ranked gene list not working

[Graeme Thorn]

Hi,

I've got log fold-changes from an RNA-seq experiment I'm trying to analyse using GSEA v 4.4.0 (build 18, Sat 8 Mar 2025) on MacOS v26.3.1, and I can't seem to load in my ranked list when running GseaPreranked. Whenever I click the arrows at the end of the box, there are no suggestions for files to load.

I have checked and the ranked list (2 column: symbol, fold-change) is loaded as a Dataset in the Object cache, so I am unsure what I might be doing incorrectly in trying to run this analysis.

I have tried to run GSEA separately on the expression values but it's only a 2 condition x 2 replicate experiment, so it throws an error that there are not enough reps to run.

Is this a bug with this build?

Regards,

Graeme

[Graeme Thorn]

Actually scrub this (above), it's because it was imported as a Dataset and not as a RankedGeneList - it needs the .rnk extension to be recognised as such.

G