Handling genes with zero expression when using gp.gsea

[looppy95]

Hello! I'm currently working on single-cell GSEA analysis using gp.gsea. In your tutorial, a subset (bdata) was created using adata[adata.obs.seurat_annotations == "CD14 Mono"].copy(), and gp.gsea was directly applied to this subset.

I have a question regarding handling genes with zero expression in the subset. Should I filter out low-expressed genes before running GSEA, or is it acceptable to directly use gp.gsea even if the subset contains genes with zero expression?

Your guidance on this matter would be greatly appreciated. Thank you!

[zqfang]

Genes with zero expression across all the cells/samples will be filtered out internally to avoid computation failure.