I have 2 questions about WGCNA on female and male datasets (tutorial II).
1-In the tutorial II shows female modules (from tutorial one) has been used vs the consensus modules from both female and male data. Does that make any difference if I use male modules vs the consensus modules? If it does, how can we decide which one should we use?
2-When you find the consensus modules, how can I export edge and node info for cytoscape? On the website, it shows it for only when we have female data.
The first tutorial on the main WGCNA tutorials page, i.e., 'I. Network analysis of liver expression data from female mice: finding modules related to body weight', is just generic and can be used for any dataset that you have.
In Tutorial II, 'II. Consensus analysis of female and male liver expression data', the steps will take you through the processing of both the male and female datasets, and then, also, the consensus analysis of these.
For exporting to Cytoscape, you just need the WGCNA::exportNetworkToCytoscape() function, as elaborated in '6. Export of networks to external software' under the first main tutorial on the WGCNA page.