search

kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
399 stars 81 forks source link

advice on LFC cutoff #46

Closed klai001 closed 4 years ago

klai001 commented 4 years ago

Hi Kevin thanks for developing the EV. was wondering if you recommend a cut off for LFC for values that are shrunk? my values are shrunk and in your vigentte you mentioned that LFC |1.5| is too stringent that's true because i cant see any labels appearing with LFC 1.5 how do we determine the LFC for shrunk values and what's your recommendation? thanks

kevinblighe commented 4 years ago

Hey @klai001, yes, the shrinkage can drastically reduce the fold-change. I think that it is okay to reduce the cut-off to absolute 1. As these are log scale, at a cut-off of even 1, the change is appreciable.

kevinblighe commented 4 years ago

Please re-open if there is still any doubt!