I have case control studies,4 different condition where I have 1 control and against which I'm have 3 comparisons to make.
I did WGCNA for individuals samples .Here I have the kept the number of genes equal in all the cases .
Now my question is whether the number of modules which are obtained from WGCNA would be similar in number if I run module preservation between two condition .
Lets say i get 15 modules in Control condition and 16 treated condition if I run module preservation the number of modules which would come would be 15+16= 31 or its independent .
The power I have kept same for both WGCNA and module preservation analysis. But Still I get different module numbers.
Any suggestion would be highly appreciated