Regarding finding hub genes using WGCNA

Dear all,

I have got the gene expression microarray dataset (about 17000 genes) of about 400 cancer samples with different cancer subtypes. I considered subtypes as traits (binary traits) and used WGCNA to find the possible modules associated with traits and to identify hub genes. I used 50% genes with the highest variance as input for WGCNA and selected signed network type. Could you please help me out with some issues?

1. As the green module was one of the associated modules with one of the cancer subtypes (trait), I try to find hub genes in this module via the criteria of GS > 0.2 & MM. green > 0.8. It returned to me 6 genes, however, when I further checked them, I found that two genes belonged to another module, not the green module. The same thing happened when I found hub genes in another associated module. Could you please tell me why it has happened? What’s wrong?

1. Regarding modules with a negative association with the binary trait, how we should interpret them especially in terms of gene expression at those modules? Here, using the signed or unsigned network is important for interpretation?

Thanks in advance