I'm interested to perform gene co-expression using WGCNA R module. I clean data for samples and remove genes that don't form any cluster. Post cleaning I perform clustering to identify different modules (40 excluding grey). Each module consist different number of genes, I generate list of genes in a output text file.
Next, I merge module that are highly similar and left with 20 modules. Further, I perform regression to identify module significant to the trait. I see the P-value and module name, which is OK.
I'm unable to move forward here with two things:
1- I don't know which modules were merged with what. Initial module clustering and gene list isn't helpful after module merging.
2. I'd like to have gene names binned in newly merged modules.
How do I make my way with these two points?