cytoscape : edge weighted layout

Question

[lagartija]

Hi,

I am working on a cytoscape network with an "edge-weighted" layout (very important, because everything is connected). Still I never manage to understand if the column I give as the edge weight value should be a distance or a similarity. The network looks quite similar whether I interpret my entry as the normalized value or as 1-normalized value.

How to explain that ? ; Thank you very much in advance !

Answer 1

[scooter]

Greetings, That definitely seems wrong to me also, unless the network is so dense that it isn't getting spread out at all, or the normalized values are being swamped by some outliers. You may want to take a look at the range of your values to see if you have a couple of extremely strong (or extremely weak edges). You may also want to consider applying a cutoff. To directly answer your question, though, if you are using the defaults (e.g. heuristic interpretation) the weight value is interpreted as a distance.

-- scooter