Question: How to adjust the parameters of WGCNA
gravatar for xie186
21 months ago by
xie1860 wrote:

I used WGCNA to construct co-expression network based on RNA_seq data from 18 samples. I got around 60 modules. Half of the modules have less than 100 genes. I selected several modules and plot the heatmap using the expression values. I found that nearly all of the modules I checked have two expression patterns. See one example below. 

My questions: is it possible that I can adjust the parameters to separate this module into two different ones? How to do that? Or it's better I do the separation myself? Thanks. 

ADD COMMENTlink modified 21 months ago by Peter Langfelder1.6k • written 21 months ago by xie1860
gravatar for Peter Langfelder
21 months ago by
United States
Peter Langfelder1.6k wrote:

I'm not sure I understand your question well, but if you get two opposite expression patterns in one module, chances are it's because you have constructed an unsigned network. Rerun WGCNA using a signed or 'signed hybrid' network. I recommend 'signed hybrid' with the same soft thresholding power as your original analysis.

See for a slightly more in-depth discussion.



ADD COMMENTlink written 21 months ago by Peter Langfelder1.6k

Thank you so much. This is exactly what I need. I'll try this. 

ADD REPLYlink modified 21 months ago • written 21 months ago by xie1860
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 234 users visited in the last hour