Details about output about carnival HOT 6 CLOSED

Hi Ansuman,

A 100 AvgAct means that a node has an average activity of 100, i.e. if you have retrieved 100 solutions from CARNIVAL that means that this node was inferred to have a +1 activity sign across all the 100 solutions. Similarly, for -100 that means that the node was inferred across all the 100 solutions with a -1 regulation sign. The AvgAct for each node is calculated as the weighted mean of the activity values it takes across all separate solutions: [n10+n21+n3*(-1)]/(n1+n2+n3) * 100, where n1 is the number of times the protein has been inferred to have an activity of 0 (or not present in that specific solution), n2 is the number of times that protein has been inferred as up-regulated/have an activity of +1, and n3 is the number of times that protein has been inferred as down-regulated/have an activity of -1, n1+n2+n3 is the total number of solutions you get.

On the other hand with T we label the target nodes or the TF's and with S the source nodes. NA's are nodes that have not been designated and which can be intermediate proteins that have been inferred or not.

Hope this helps.

Cheers,
Enio

from carnival.

It does help a lot! Another question is that in the log file it says Solution pool: 1 solution saved. Does this contradict with 100 AvgAct(meaning +1 activity across 100 solutions)? Even if not, don't we expect to save more solutions?

log file: 483081-slurm.txt

from carnival.

Hi Ansuman,

No, the AvgAct represents the weighted average activity across all the solutions you get and it was made so it will always take a value between -100 to 100 no matter how many solutions you get (see the formula I gave on the previous comment). An AvgAct=100 simply means that in all the solutions you get a protein has been inferred to have an activity of +1. Otherwise if in all solutions the inferred protein has an activity of -1, then the AvgAct will be -100. This is true no matter whether you get 1 single solution, 100 or any othe number depending on the parameters you set when you run CARNIVAL. The AvgAct could have of course also been made to take a value between -1 and 1, but I thought it is best to put the limits -100 to 100 since we usually by default like to get 100 solutions and this would make interpretation a bit easy:). You can of course as well scale AvgAct from -1 to 1 if it makes interpretation easier for you.

Cheers,
Enio

from carnival.

Thank you Enio! Now it is much clear. I understand differences in scale, yet I suspected that having only one solution as a results wouldn't be reliable(as in the log file). But I do not think that I can get more solutions. Because I am not giving inputObj, I think this is the best I can get without feeding the algorithm with potential targets of perturbations.

from carnival.

Hi Ansuman,

I think the best thing one could do is either:

a) Give it a bit more time for the analysis to run by changing the timelimit parameter, or
b) Put a gap value a bit higher than the one you are getting. You can check the current minimal gap value either on the log file or in R when CARNIVAL finishes running.

Indeed one single solution might not be that much of a reliable solution :)

Cheers,
Enio

from carnival.

Aha! That sounds like a great solution!
I am closing the issue for now.

Many thanks :)

from carnival.