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netZoo / netZooPy

netZooPy is a network biology package implemented in Python.
https://netzoo.github.io/
GNU General Public License v3.0
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Initialization of protein-protein interaction in Panda #333

Closed janursa closed 5 months ago

janursa commented 11 months ago

I noticed in this line of code, a value of 1 is assigned to the self-interaction of proteins. I am concerned about the implications of this assignment on the normalization of PPI values. In my dataset, the PPI values are relatively small, and this assignment of 1 to self-interactions prior to normalization could render these values negligible. Is this assignment a necessary step before normalization, or should there be a specific format for the PPI values to address this issue?

marouenbg commented 9 months ago

Hi @janursa ,

Apologies for the delay. This is only effective when you don't provide a PPI network. In this case, we need to have an neutral element in the algorithm (identity matrix), to be able to compute the final network without a PPI influence.

Marouen

marouenbg commented 5 months ago

Feel free to repoen @janursa if you have other questions.