Hi all, I have a basic doubt regarding the creation of weighted correlation network in WGCNA-the first step. Iam doing it for the first time and want to do for my proteomics data which is preprocessed. I have spectral counts and normalised spectral abundance factors for the genes(proteins with gene ids) for the control and mutant with three replicates each. From what i do understood, first i need to transpose my data so genes are in the columns. second i need to calculate pearson correlation for the genes , than do soft threshholding and calculate mean connectivity. It would be really helpful to let me know if my approach is right or detailed r script for the creation of weighted correlation network. One more imporatnt doubt is how to select the database for the tomato for coexpression data analysis. For my data i have done the analysis with itag4.1. Thank you in advance.