After pruning, none of the gene sets passed size thresholds.

[Neda Mahboobnia]

Hi, I have a gene list of 80, downregulated in my treated cells. two groups: control and treated. 4 replicates per group. I constantly get this error. I have selected symbol -hallmarks as gene set database,  No collapse, Permutaion type: gene set, chip platform: gene symbol with remapping. Collapsing mode: sum of probes.

Pls give me guidance 

Thanks

[Anthony Castanza]

Hi Neda,

GSEA needs a full dataset of all expressed genes, 80 just isn't enough to reasonably analyze sets with respect to the expression universe like GSEA is designed to do.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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