I have 19803 genes and 201 samples with raw counts data. I have used DEseq2 package to get normalised counts which is given as input to WGCNA.
Before that I have using filtering step in deseq2 package, with which I kept genes only with more than 20 counts in total for each gene. With this I have 18000 genes for WGCNA.
Scale free topology fit index gave a plot like below:
1) From that do I need to take softPower 6 or 7?
2) Is there a way to reduce the number of input genes with some other strict filtering? [Ofcourse I could take only top 50% variable genes and do co-expression analysis, but like that the gene I'm interested in filtered out]