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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 .

Weighted gene network coexpression analysis (WGCNA) reveals stage-specific modules (gene network) in neonatal left and right ventricles

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  • $\begingroup$ How many samples do you have for each condition (and for the controls)? This method works well if you have enough homogeneous samples of each condition. The official tutorials are here, maybe you find them more informative $\endgroup$ – llrs Sep 16 '19 at 9:10
  • $\begingroup$ i have 54 samples in control and 50 samples in MDD as one of the condition $\endgroup$ – krushnach Chandra Sep 16 '19 at 9:59
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    $\begingroup$ And the other conditions BPD and SCZ? With those numbers you can do an analysis of each condition and then compare the clusters. Did you read the tutorials of the official site? Where they helpful or do need still some clarification? $\endgroup$ – llrs Sep 16 '19 at 10:01
  • $\begingroup$ they are similar somewhere between 50-60 sample each .i have followed this one horvath.genetics.ucla.edu/html/CoexpressionNetwork/… $\endgroup$ – krushnach Chandra Sep 16 '19 at 10:28

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