Hey,
first: thank you for the package along with the data comprehensive book/vignette, it's great!
I was digging a bit deeper in the original Reactome analysis provided by the web-tool and there p-values are corrected by benjamini-hochberg and can be reported and subsequently filtered. Is this correction already implemented in the reactomePA::enrichPathway() function and hence pAdjustMethod = "BH" would be 'double correction'?
I am asking, because setting pAdjustMehthod = "none" give very comparable results to the webtool result, whereas leaving it to "BH" seems to be much more stringent.
What would you suggest?
Kind regards
Thorben
Hey,
first: thank you for the package along with the data comprehensive book/vignette, it's great!
I was digging a bit deeper in the original Reactome analysis provided by the web-tool and there p-values are corrected by benjamini-hochberg and can be reported and subsequently filtered. Is this correction already implemented in the reactomePA::enrichPathway() function and hence pAdjustMethod = "BH" would be 'double correction'?
I am asking, because setting pAdjustMehthod = "none" give very comparable results to the webtool result, whereas leaving it to "BH" seems to be much more stringent.
What would you suggest?
Kind regards
Thorben