Low NES for high enrichment plots

[Nupur]

Hi, 

I am doing a GSEA analysis for my RNA-Seq data. 

I am getting high enrichments in the genesets, but somehow the NES values are low - about 1.5 ~. 

The enrichment plot ES values are going upto 0.9 - 1.

Can you tell why the NES values are low ? 

Thanks,

Nupur

[Castanza, Anthony]

Hi Nupur,

The NES value is calculated from the true enrichment score and the null distribution generated by the permutation test. A lower NES indicates that there are likely many values found in this null that are similar to the true enrichment score. This is also likely to impact the NOM pValue/significance statistics returned by the software. You can see a plot of the null distribution at the very bottom of the results page for each gene plotted gene set.

 

Let me know if you have any more questions

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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