Large number of significant genes

[LeonardosMageiros]

Large number of significant genes

[AdmiralenOla]

Hi Leonardos,

I doubt this would change much by supplying a phylogenetic tree to scoary.

The Fisher/Bonferroni p-values are assuming that your isolates are all equally related to each other, or at least that there's no systemic pattern of relation between them that could influence the association between genes and traits. This of course is never the case in real life.

It is likely that your data has a high degree of pseudoreplicates, isolates that are clustered on a phylogenetic tree and that share a lot of their genetic make-up, as well as phenotypic characteristics. I don't know so much about S. aureus, but I'm assuming you have nearly complete separation by host? In other words, all the human isolates cluster together, all the dog ones (or whatever host you have), etc?

In that case it's not unheard of to find that many genes associated with each of the host types. Just remember that there is not necessarily any causal link between the genes you find and specialization to the host niche.

All the best,
Ola