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help > RE: The abnormal random and actual sizes during permutation
Feb 16, 2022 11:02 PM | Andrew Zalesky
RE: The abnormal random and actual sizes during permutation
Hi Gucy,
- If the observed (actual) size and the size under the null hypothesis are 0, then it makes sense that the p-value is 1. This means that you cannot reject the null hypothesis. This is consistent behaviour. I am not sure what you mean by "it still showed a subnetwork even though the P-value is 1". If you put a p-value threshold of 0.05, no network should be shown in this case.
- If you are findings that all edges from a massive network that remains significant, even for very high thresholds, it is likely that your design matrix is not specified correctly. For example, you might be detecting a mean effect rather than a between-group difference. Consider checking the design matrix.
Andrew
Originally posted by Chanyuan Gu:
- If the observed (actual) size and the size under the null hypothesis are 0, then it makes sense that the p-value is 1. This means that you cannot reject the null hypothesis. This is consistent behaviour. I am not sure what you mean by "it still showed a subnetwork even though the P-value is 1". If you put a p-value threshold of 0.05, no network should be shown in this case.
- If you are findings that all edges from a massive network that remains significant, even for very high thresholds, it is likely that your design matrix is not specified correctly. For example, you might be detecting a mean effect rather than a between-group difference. Consider checking the design matrix.
Andrew
Originally posted by Chanyuan Gu:
Hi Andrew,
I compared two groups using NBS and T-test, but the random and actual sizes are hard to explain. For one direction (e.g., 1 -1), the random and actual sizes are both 0, and the p-value is 1. However, it still showed a subnetwork even though the P-value is 1 after the permutation. For another direction (e.g., -1 1), the random and actual sizes are both large, almost over 2000. The subnetwork that NBS reported consisted of all nodes (90) and 3438 edges. I also adjusted the threshold from small (e.g., 1) to large values (e.g., 15), but the results were the same for both directions.
I have already used NBS for a while, but I have never met this issue before. Hence, I am lost here, could you please give me some suggestions to solve this issue? Thank you so much!
Best,
Gucy
I compared two groups using NBS and T-test, but the random and actual sizes are hard to explain. For one direction (e.g., 1 -1), the random and actual sizes are both 0, and the p-value is 1. However, it still showed a subnetwork even though the P-value is 1 after the permutation. For another direction (e.g., -1 1), the random and actual sizes are both large, almost over 2000. The subnetwork that NBS reported consisted of all nodes (90) and 3438 edges. I also adjusted the threshold from small (e.g., 1) to large values (e.g., 15), but the results were the same for both directions.
I have already used NBS for a while, but I have never met this issue before. Hence, I am lost here, could you please give me some suggestions to solve this issue? Thank you so much!
Best,
Gucy
Threaded View
| Title | Author | Date |
|---|---|---|
| Chanyuan Gu | Feb 16, 2022 | |
| Andrew Zalesky | Feb 16, 2022 | |
| Chanyuan Gu | Feb 17, 2022 | |