Hi,
I am working on WGCNA for DNA methylation EPIC array data. And I selected the top 400,000 CpG probes with high variance across 71 samples for WGCNA analysis. The soft threshold returned by the WGCNA system is sft$powerEstimate=7. In the end, I got 241 modules. I feel a little strange about how I can get so many modules. When I checked back, I realized that when I used the system's recommended threshold (7), there would be a very high degree of connectivity(mean.k.=10,700). In this case, should I still stick with the system-recommended threshold or find another suitable one myself? Thanks.
powers = c(c(1:10), seq(from = 12, to=35, by=2)) sft=pickSoftThreshold(datMethy,powerVector=powers,verbose=5,networkType="signed")
bwnet = blockwiseModules(datMethy,corType="bicor",maxBlockSize=20000,deepSplit =2, networkType="signed", power=7, minModuleSize=50, reassignThreshold=0, mergeCutHeight=0.25,numericLabels=TRUE, saveTOMs=TRUE, pamRespectsDendro=FALSE, saveTOMFileBase="methyTOM",verbose = 3)
