Hi, I am trying to run WGCNA on RNA seq data and I end up with few modules. I've seen a similar post but unlike those data, mine present a better scale free topology index. I run 3 different databases and always have similar results, I am wondering if I am missing something.
Here is the code:
adjacency = adjacency(datExpr, type = "signed", power = 5) TOM = TOMsimilarity(adjacency, TOMType = "signed", TOMDenom = "mean", suppressTOMForZeroAdjacencies = FALSE, verbose = 5)
The count matrix was created from FASQT files in Galaxy using Bowtie2/HTSeq. Then all samples were normalized using DESeq2 and exported. Further filtering based on counts, row variance and protein coding genes, as well as Log2 transformation were conducted in R. Final number of genes was 14692