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AdmiralenOla / Scoary

Pan-genome wide association studies
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Significance of the worst_pairwise_p #108

Open plasmid02 opened 1 year ago

plasmid02 commented 1 year ago

I am interested in finding out how to interpret the significance of a gene where the best_pairwise_p is < 0.05 or lower but the worst_pairwise_p is non-significant. Assuming this gene is below the Bonferroni threshold , should this be considered a judgement call?

MrTomRod commented 1 year ago

I wrote a section on this topic on Scoary2's wiki!

sydelstan commented 6 months ago

I have read the great wiki article by @MrTomRod but I am still not sure how to understand the situation described by @plasmid02

MrTomRod commented 6 months ago

Can you share all the relevant p-values, and if possible a phylogenetic tree which contains all relevant information (gene and trait)?