Re: Heatmap Plots

[Adeyeye Haastrup]

Hello Anthony, I hope my message meets you well. When we Run GSEA, is there a way to limit the heat maps generated to about 20 genes or whatever number we pick so that we don't get a very long list of genes int he heat map but the top ones?
Looking forward to your reply,
Best regards, 
Ade.

[Anthony Castanza]

Hi Ade,

GSEA's heatmap plotting is pretty limited and the software does not have the ability to adjust the number of marker genes plotted in the heatmaps in this way. You would need to use external software, with row-normalized color assignments in order to best match the visualization that GSEA produces.

Sorry I couldn't be of more help here!

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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