I'm trying to create an unsigned coexpression network for some RNA-seq data (number of genes = 20555, number of subjects = 379). I have already processed the data through TMM/Voom. When I tried to create the coexpression network (using the same commands as in the WGCNA tutorials), specifically the pickSoftThreshold function, my data does not reach 0.90. It actually only reaches ~0.70. My understanding of the purpose of raising my data to a beta was to remove any noise embedded in the data. However, haven't I already done this by running TMM/Voom?
I suppose I have 2 main questions:
1) Could someone explain the difference of raising RNA-seq data to a soft-thresholding beta versus normalizing RNAseq data with TMM/voom?
2) Since the data is not reaching 90% to determine a soft threshold beta, what should I do to generate a coexpression network?