I have done a WGCNA (weighted gene co-expression network analysis) analysis for various brain disorders. So along with control, I have 3 different disorders such as BPD, MDD and SCZ. Now I have to find out what sort of modules are preserved between the control and disease condition.
I have cited a paper where they have done module preservation analysis. Now I have checked the WGCNA or website they do have given example of mouse male and female liver module preservation.
I am stuck at this do I need both the expression data together to do module preservation analysis? Or do I first have to run WCGNA on both the data sets and then look for?
For example if I want to look at what are the modules preserved in CTRL and BPD condition.
I have followed this tutorial section 12.5 Module preservation between female and male mice
where it reads both male and female data together which is bit confusing
maleData = read.csv(file.path(data.dir, "LiverMaleFromLiverFemale3600.csv"))
Any suggestion would be really helpful .