I have FPKM data for 6 samples (3 control, 3 treated). I tried to construct a co-expression network using WGCNA. I used the following code below however my adjacency matrix obtained from expression data in WGCNA returns NA. I don't understand why this is happening. Any suggestion will be highly appreciated. I have attached the picture of matrix below.
Thank you
library(WGCNA) library(flashClust) enableWGCNAThreads(nThreads = 64) dat=read.csv("FPKM_rep.csv") names(dat) demo=as.data.frame(t(dat[,-c(1)])) names(demo)=dat$Genes powers = c(seq(1,20,by=1)) sft = pickSoftThreshold(demo, powerVector = powers, networkType="unsigned",corFnc = cor, verbose=5) par(mfrow = c(1,2)) cex1 = 0.8 plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])sft$fitIndices[,2],xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n",main = paste("Scale independence")) text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])sft$fitIndices[,2],labels=powers,cex=cex1,col="red") abline(h=0.80,col="green") plot(sft$fitIndices[,1], sft$fitIndices[,5],xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n",main = paste("Mean connectivity")) text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1,col="red") softPower = 8 adjacency = adjacency(demo, power=8, type="unsigned")
