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help > RE: Exclude nodes from the matrix for analysis
Dec 8, 2018 01:12 AM | Andrew Zalesky
RE: Exclude nodes from the matrix for analysis
Hi Marieke
the size of nbs.GLM.y and nbs.NBS.test_stats will not change if values are set to zero. However, for the purpose of the NBS, the values with a t-stat of zero are effectively excluded from statistical inference. This is the same as if you were to explicitly remove the values from the connectivity matrix. Note that this will not be the case for the FDR option. For FDR, all connections will be included, irrespective of whethter they are zero or not.
I suggest adjusting your connectivity matrices by removing the rows/columns that correspond to nodes that you want to exclude.
Andrew
Originally posted by Marieke van der Schaaf:
the size of nbs.GLM.y and nbs.NBS.test_stats will not change if values are set to zero. However, for the purpose of the NBS, the values with a t-stat of zero are effectively excluded from statistical inference. This is the same as if you were to explicitly remove the values from the connectivity matrix. Note that this will not be the case for the FDR option. For FDR, all connections will be included, irrespective of whethter they are zero or not.
I suggest adjusting your connectivity matrices by removing the rows/columns that correspond to nodes that you want to exclude.
Andrew
Originally posted by Marieke van der Schaaf:
Dear Andrew,
Thank you for your quick response. I'm running the analysis with 500.000 permutations, it just takes ages... Thanks for the warning.
I replaced the excluded node-values to zero, but still nothing seems to change. I attached the nbs structures for the full matrix and selected matrix in a zip file. Can you tell me if the selection is correct? Maybe I'm just missing something?
I am interested in testing connectivity from network e.g. A (7 regions) to network A, B, C and D. This should reduce the nr of comparisons to 581 (7*84 regions) compared to 3486 when using the full matrix (84x84 regions).
For this, I kept all rows and columns of network A (see datafile attached) in the matrix and set al other edges to zero, I also tried with only keeping the rows, but that gives the same results too. I now see that e.g. all test_stats are zero for those edges that I excluded, but the size of these matrices (e.g. nbs.GLM.y or nbs.NBS.test_stat) have not changed. Is their any way I can check final number of comparisons that the program uses for correction?
Best, Marieke
Thank you for your quick response. I'm running the analysis with 500.000 permutations, it just takes ages... Thanks for the warning.
I replaced the excluded node-values to zero, but still nothing seems to change. I attached the nbs structures for the full matrix and selected matrix in a zip file. Can you tell me if the selection is correct? Maybe I'm just missing something?
I am interested in testing connectivity from network e.g. A (7 regions) to network A, B, C and D. This should reduce the nr of comparisons to 581 (7*84 regions) compared to 3486 when using the full matrix (84x84 regions).
For this, I kept all rows and columns of network A (see datafile attached) in the matrix and set al other edges to zero, I also tried with only keeping the rows, but that gives the same results too. I now see that e.g. all test_stats are zero for those edges that I excluded, but the size of these matrices (e.g. nbs.GLM.y or nbs.NBS.test_stat) have not changed. Is their any way I can check final number of comparisons that the program uses for correction?
Best, Marieke
Threaded View
| Title | Author | Date |
|---|---|---|
| Marieke van der Schaaf | Dec 4, 2018 | |
| Andrew Zalesky | Dec 5, 2018 | |
| Marieke van der Schaaf | Dec 6, 2018 | |
| Andrew Zalesky | Dec 8, 2018 | |