I am a user of WGCNA found it really useful for my RNA seq analysis! Currently, because of my research interest, the data I am planning to work on is qPCR data, with much smaller number of genes (from around 30 genes), with relatively big sample size (1000 samples, highly heterogeneous). Apparently I could not get scale free topology, and identifying any big module, which I think is because of the small number of genes. I looked up a lot but could not find anyone asking about using WGCNA on small gene sets. (yes most datasets are now big data..)
Do you think WGCNA is still applicable for such a small datasets? I am planning to use power = 10 and detect any modules with size 5 genes in the module. But any suggestion on parameter adjustment or the usage of the package in this situation?
I really appreciate your time and any suggestions!!!