Misuse NES in PROGENy zscores

saezlab / transcriptutorial

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL

https://saezlab.github.io/transcriptutorial/

GNU General Public License v3.0

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Misuse NES in PROGENy zscores #11

Closed jperales closed 1 year ago

jperales commented 3 years ago

https://github.com/saezlab/transcriptutorial/blob/81c76439d0c2ad7c451aefab332029ffe1034a03/scripts/03_Pathway_activity_with_Progeny.Rmd#L132-L160

Reference above. I think using NES for PROGENy z-scores is not correct. If so, Should we correct this? Thanks

Javier

adugourd commented 3 years ago

Ah yes this is confusing. Actually it is a normalised enrichment score. Nes and z-score are the same for weighted mean enrichment strategy, which is what is done in progeny.

I'm not sure how to make it less confusing though.