WGCNA threshold values

Question

[pr2009]

Hi Everyone,

I am using WGCNA for generating modules for my non-coding RNAseq data

I doing a separate analysis for 13 different tissues. My question is what soft threshold value will be ideal and if I am using different threshold value for different tissues will it affect my overall analysis.

My sample size range is between 80-500 in different tissues.

Thank you

Answer 1

[Kevin Blighe]

My question is what soft threshold value will be ideal

Generally choose the first value that passed 0.9 on the y-axis. This is, more often than not, 6 or 7.

Kevin