Hi, I did RNA-seq analysis and Im planning to analyze with WGCNA, I have seen several papers with trait data, but I have a large RNA-seq sampling but few trait data. I was wondering if it is valid do WGCNA just with the expression data and not including any trait data.

Thanks

You don't need (and can't use, AFAIK) trait data for module creation, so if your goal is to just identify modules of co-regulated genes, then your'e good.

Often people want to the associate the activation/expression-level of modules to "traits" but that's a downstream step ...