adjusted p-vlaue in genome_by genome_overview files

[Former user]

The adjusted p-value is not significant they are range from 0.5 to 1, what does the adjusted p-value mean?

Thanks!

Ning

[Ben Bolduc]

Hi Ning,

Sorry I couldn’t get to this earlier. The adjusted p-value is an intermediate transformation in order to calculate the overall topology score. With the topology score calculated as: quality value X adjusted p-value. This topology score is how much confidence vContact2 has in regard to the structure of the VC. It takes into account many aspects of the network itself (number of nodes in VC, node edge weights, etc) and gives a “feeling” of a genome within the network. Low scores indicate less “confidence” in the position of a node within the network, whereas high scores have more confidence. I don’t like to use “confidence” or “p-value” or similar terms to describe exactly how this value functions, mainly because low scores can be 100% biologically viable but not necessarily significant. But because of a low number of genomes in the VC, or weak connections between their members, they get scored low. A combination of the topology score and genus confidence score gives an indication of overall confidence of placement and classification.

Cheers,

Ben