help > RE: edges counted twice in gPPI
Jan 22, 2022  05:01 PM | Alfonso Nieto-Castanon - Boston University
RE: edges counted twice in gPPI
Hi Laura,

Regarding (1), yes, NBS statistics are derived from the results of randomization/permutation simulations so they remain valid irrespective of how the networks are defined (e.g. as sets of connected nodes from directed or indirected graphs). I am not sure what you mean by "how do the statistics work if both directed edges are counted", the network-intensity measure from a network is computed by summing the number of suprathreshold edges within the network. For example, if a network of two areas A&B is identified and A->B is significant and B->A is not then the network intensity is 1, if both are significant then the network intensity is 2. The same logic applies to any other network computed during the permutation/randomization runs, so the final network-intensity statistics are derived by comparing the intensity of this network to the distribution of network intensities expected if the null hypothesis was true. 

And regarding (2), the interpretation of directionality differences in gPPI analyses is debated, unless you want to make a specific case about the directionality of specific connections within any of your significant networks I would generally recommend simply describing each network in terms of the nodes/ROIs within each network and the connections between them, rather than focusing on the specific directionality of these edges/connections (but it is perfectly fine either way)

Hope this helps
Alfonso
 
Originally posted by Laura Jett:
Thank you for your reply! We understand why we end up with an asymmetric matrix; however, we are still unsure on a few points:
  • Does the matrix need to be symmetric for network-based statistics to be valid? If network-based statistics are valid with an asymmetric matrix, then how do the statistics work if both "directed edges" are counted?
  • What is the interpretation? For example, if A → B is part of a significant cluster, can we infer the directionality of this edge?
Do you know of any implementations of network-based analysis that use gPPI as inputs so that we may see how others have handled these kinds of questions? We really appreciate all of your assistance with this matter!

Kind regards,
Laura

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TitleAuthorDate
Laura Jett Nov 9, 2021
Rany Abend Jan 10, 2022
Rany Abend Jan 18, 2022
Alfonso Nieto-Castanon Dec 3, 2021
Laura Jett Jan 5, 2022
RE: edges counted twice in gPPI
Alfonso Nieto-Castanon Jan 22, 2022
Rany Abend Jan 22, 2022
Alfonso Nieto-Castanon Jan 22, 2022
Rany Abend Jan 23, 2022
Rany Abend Dec 1, 2021