Hi Rahul, 

this is most likely due to your use of a lenient primary threshold (t=1.8). 

If the sample size is not sufficiently large, t=1.8 will not ensure that p<0.05 and thus it is unsurpising that several connections do not have p<0.05.

I recommend increasing the primary threshold. Perhaps try t=3.  

Andrew

Originally posted by Rahul Biswas:

Hi,

Thank you very much for this great tool. I have a question, as follows. 

I performed two analyses after obtaining subject-specific directed functional connectivity: 1) used dNBS with primary threshold 1.8, 10K permuations, and size based on extent, to obtain a subnetwork with lower strength in diseased group compared to healthy group at significance level 0.05. 2) obtained edge-wise p-values for lower strength in diseased group compared to healthy group using Welch's t-test for each edge in the directed functional connectivities. 

However, the subnetwork obtained in analysis 1 is not a subset of edges having edge-wise p-value less than 0.05 in analysis 2. Isn't this wierd? I would really appreciate an explanation.

Some more detail: Only two edges in the subnetwork in analysis 1 have edge-wise p-value less than 0.05 in edge-wise Welch's t-test (analysis 2).

Thank you very much for explaining this.

Best regards,
Rahul