Frequently Asked Questions
Q: My hub degree threshold (
-g) is 20 but some of the hubs reported only have 10 interactors!
A: Hubishness is based on the supplied network, after complexes are decomposed. If your file has complexes in it (the word "complex" appears in the name) then it'll be decomposed automatically. If one of your nodes is part of a very big complex, it's going to have a lot of interactors, so it'll count as a hub.
Q: It says "no contextually relevant nodes found" even though my file has context in it!
A: Check which attribute you're specifying for
-a. Make sure your xgmml file has cross-reference information (you must use the InnateDB/Cerebral format, shown here).
Q: I supplied a text file with a list of genes and context (
-n), but the context isn't getting added to the network (network builder mode).
A: Your file needs to be labeled with column names or else the script won't know where to look for your data. You'll need an 'ens' column and a 'pVal' or 'FC' column. Case matters, and make sure if you're using the default delimiter that your file has proper tabs (\t), not whitespace. If that doesn't work for you, use commas and specify with the
Q: I supplied a list of genes and the script tells me "No contextually relevant genes found" and the xml shows context is empty!
A: Check for stray tabs in your input file.
Q: Some of my hubs have more interactors in the network than they do in the universe mitab file. Is this a bug?
A: If your network has complexes in it (node name contains "complex") then that complex is decomposed by default, and every node connected to it is assumed to interact with every other node connected to it. So Complex A:B:C:D is is decomposed, and interactions A:B, A:C, A:D, B:C, B:D, etc are tallied for every node. B:D may not exist in the mitab file, but because of the interaction with the complex, it's counted in your network. If you'd prefer not to decompose complexes this way, call with -spoke to skip this step.