TOMplot in WGCNA

Question

[vivien.wee16]

Hi,

I am trying to construct a coexpression network using WGCNA. Everything was fine until I wanted to make a TOMplot. When I was calculating TOM using TOMsimilarityFromExpr function, the dataframe that it returned was full of NaNs and of 1s diagonally across the dataframe. The only difference I made compared to the WGCNA tutorial was that I changed the maxModuleSize in blockwiseModules to a number (12000) so that all the genes in my data could be in one block, instead of 3 using the default maxModuleSize. Does anyone have any idea why this happened?

Thank you!