Change of parameters for statistical significance

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Jun 29, 2019, 2:06:16 AM6/29/19

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Hi Matt

I am doing subnetwork analysis using hotnet2 but not getting p-value<0.05 in any of the four delta directories.

What should I do? Are there some parameters which I need to change/optimize and run the algorithm again. Please suggest.

With regards

Shivangi Agarwal

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Jun 29, 2019, 4:43:42 AM6/29/19

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Hi Shivangi,

I think that you asked this question last year. Please check this forum for similar questions and answers.

Best,

Matt

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Jun 29, 2019, 4:52:05 AM6/29/19

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Ya, but I need to know can I change number of heat permutations (hp) or np, will it affect p-value? (not in lastly raised questions).

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Jun 29, 2019, 5:23:42 AM6/29/19

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Hi Shivangi,

More permutations are better, but they will not substantially change the p-values. Please check the HotNet2 paper for details.