How can we be sure that this module preservation is comparing the same module genes in the two groups?

Question

[Gail]

I did two runs of WGCNA one with my control group comparing 2 time points and another looking at the treated group comparing two time points.

I then used the data expression data and module lists from the two WGCNA runs as my input for my module preservation-- but when I double checked, it doesn't look like the same genes are in the same module colors. How can we be sure that this tool is comparing the same module genes? Because even if they have the same module color names, I am seeing different gene names in the modules in one group and the other.

Please help.

[andres.firrincieli]

Because even if they have the same module color names, I am seeing different gene names in the modules in one group and the other.

the module preservation analysis try to replicate the modules of the reference group (eg control group) in the test dataset (eg treated group) and viceversa.

have a look at this paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001057

[Gail]

Thank you for your response-- so basically, we are not comparing the modules in each data set, but rather look at the reference set and see if those modules are preserved in the test set? Because for example, my black module in the reference set compared to my test set has a really high z-score which would mean it is highly preserved, but when I look at the genes in the black module, none of those show up in the black module of my test set. So how are they even comparing it?

[Ram]

Hi,

Why did you open a new post with the exact same content? wgcna module preservation