Rankings off by one

[Blobby]

I'm noticing that whenever I run preranked GSEA, the rankings in the reports for different genes are one lower than the rankings in the RNK file. For example, the details page for a gene set says a gene is ranked 28, but when I go to the RankedListViewer in the software for the list I used, the same gene is shown with a ranking of 29.

[Anthony Castanza]

Hello,

GSEA uses zero-based indexing for the ranked list. This is because GSEA is a java based application, and Java natively indexes arrays starting at zero, Python also uses this convention. Some software artificially "corrects" this when displaying to users, but GSEA doesn't.

-Anthony

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

On Tue, May 27, 2025, 8:25 AM Blobby <flippe...@gmail.com> wrote:

I'm noticing that whenever I run preranked GSEA, the rankings in the reports for different genes are one lower than the rankings in the RNK file. For example, the details page for a gene set says a gene is ranked 28, but when I go to the RankedListViewer in the software for the list I used, the same gene is shown with a ranking of 29.

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[Blobby]

Great, thanks for the info. Just wanted to make sure I wasn't do anything wrong.