RANK METRIC SCORE

[Bernhard]

Dear all,

how ist the RANK METRIC SCORE calculated and what does this score declare?

Is there an evidence for significance?

Thank you in advance,

best

Bernhard

[Anthony Castanza]

Hi Bernhard,

 

I’m not sure exactly what you’re asking here. GSEA internally calculates a metric by which the gene expression is differentially ranked between two phenotypes, by default this uses the signal to noise ratio, a metric which incorporates information about the magnitude of the mean change between the phenotypes and the standard deviation of the change. The options for ranking metrics built into GSEA are described in the relevant section of our user guide: https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Metrics_for_Ranking

GSEA is not concerned with the significance of any individual gene’s change per-se, rather, it uses all information about all the genes’ changes “significant” or not, to determine if a gene set as a whole is significantly perturbed.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/38a195d2-4050-4e5a-b351-180fa3271ba8n%40googlegroups.com.

[Bernhard]

Thank you for answering my question, Anthony! My question concerned the value "score" of the output file "ranked gene list_...xls with name of the gene, title and score after running a gene set analysis.

[Anthony Castanza]

Ah, I see. That output file contains the ranking value that GSEA calculated internally using the selected ranking metric.

-Anthony

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

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/47b264d2-1300-4b17-9f05-806eb9a7b76fn%40googlegroups.com.