I am performing the network analysis with WGCNA and at the very last step I have to export the network file in VisANT readable format in order to visualize the gene network in external software VisANT.

But the problem is whenever, I am exporting gene network from R version 3.6.1 the gene ids are replaced with "NA", I dont have any clue what is problem with that. Also i am attaching the image of unexpectedoutput file .

I am following WGCNA tutorial by Steve Horvath, the commands are as follows with some modification according to my data:

Recalculate topological overlap

TOM = TOMsimilarityFromExpr(datExpr, power=8)

annot = read.csv(file = "GeneAnnotation.csv"); module = "darkolivegreen"

Select module probes

probes = names(datExpr) inModule = (moduleColors==module); modProbes = probes[inModule]; probes = names(datExpr) inModule = (moduleColors==module) modProbes = probes[inModule]

Select the corresponding Topological Overlap

modTOM = TOM[inModule, inModule]

Because the module is rather large,

we focus on the 20 top intramodular hub genes

nTopHubs = 20

intramodular connectivity

vis = exportNetworkToVisANT(modTOM, file = paste("VisANTInput11-", module, ".txt", sep=""), weighted = TRUE, threshold = 0)

kIN = softConnectivity(datExpr[, modProbes]) selectHubs = (rank (-kIN) <= nTopHubs)

vis = exportNetworkToVisANT(modTOM[selectHubs,selectHubs], file=paste("VisANTInput12-", module, "-top20.txt", sep=""), weighted=TRUE,threshold = 0, probeToGene= data.frame(GeneAnnotation$GeneId, GeneAnnotation$Gene start (bp)))

Does any one has a clue what i am doing wrong? or is it some installation problem with R.

All suggestions are welcome.

Thank you in advance.