Heatmaps missing

[shamima]

Hi Anthony,

I got the GSEA results by using GSEA-preranked for my bulk RNA seq data. I used DE gene sets and it came from day4 flu data. In my HTML file, I can see the Enrichment plot, genes list, and random ES distribution but not heatmaps. Could you let me know how can I get it for specific hallmark MSigDB?

Thank you,

Shamima

[Anthony Castanza]

Hi Shamima,

I'm not exactly sure what you're asking about. What do you mean by you used "DE gene sets"?

If you used the Hallmarks gene sets, then the heatmaps should be on the results page for a given set. If That set didn't generate plots because it wasn't high enough on the ranked list, then it won't have a heatmap. In that case, you can look under advanced fields for the parameter to determine the number of top sets to plot. Increasing that might cause the sets you're interested in to plot.

If that isn't the issue, please send me a screenshot of what you're seeing so I can better understand the issue here.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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