WGCNA module interpretation question

Question

[Anny]

I am using WGCNA to generate gene co-expression network. I am confused about the how to interpret gene module colors. My understanding is, different modules will have different color. So the downstream analysis could be based a specific colored module such as blue. However, the cluster dendrogram figure show that different modules( which are not close to each other and not merged together) could have the same color, for example, there are several modules with color blue. I have been trying to find the answer in manuals, but couldn't figure out.

Could someone give me some ideas. Appreciate your help!

Alexie

cluster dendrogram figure:

Answer 1

[Kevin Blighe]

You should check how many modules have actually been identified. The number may not corroborate with the colours that you see. From what I understand, WGCNA only displays a certain number of colours, after which it will 're-use' some of these when there are more modules than there are colours. Our eyes are limited in the number of colours that they can distinguish - a human 'flaw'.

Also, you may consider modifying (increasing) your dynamic tree 'cut height', as it does appear that you have too many modules.

Kevin