Questionable results about catastrophy HOT 1 OPEN

Hi Camilo,

Sorry for the late reply, i've been away for a while.
James would be the best person to talk to about interpreting the results etc, the concept and model design was theirs.
Send them an email ([email protected]) as they don't really use github.

As a quick response, yes i agree that it's odd for this to be clustering with the biotrophs.
From a techical point of view the only thing that could artificially bias the results is if you have a particularly large genome/proteome, as the CAZyme counts weren't scaled before the PCA and many of the biotrophs used have bigger genomes. That's assuming that I haven't made a mistake somewhere on the software side, but i think it's all ironed out now. Otherwise the model really just summarises data, so what you're seeing is a genuine similarity to the biotrophs in terms of CAZyme content.

My initial thought would be that potentially there is an expansion (or depletion) of some CAZyme families more commonly associated with biotrophy. I'd be looking at the PCA loadings and CAZyme counts of those species and yours to see what is causing them to be placed close together.
James should be able to help you do this (I don't work for them anymore).

All the best,
Darcy

from catastrophy.