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WGCNA: the export files of exportNetworkToCytoscape with hubgene lost

I want to choose top 20 hub genes to visualize in the cytoscape,but the hub gene was lost, there are only 19 genes in my export files. Here is my codes :

modules = c("lightcyan")
probes = names(datExpr0)
inModule = is.finite(match(moduleColors, modules));
modProbes = probes[inModule];
modGenes = annot$description[match(modProbes, annot$GeneID)]
modTOM = TOM[inModule, inModule]
dimnames(modTOM) = list(modProbes, modProbes)
nTop = 20   
IMConn = softConnectivity(datExpr0[, modProbes]);
top = (rank(-IMConn) <= nTop)
cyt = exportNetworkToCytoscape(modTOM[top,top],
                               edgeFile = paste("CytoscapeInput-edges-", paste(modules, collapse="-"), ".txt", sep=""),
                               nodeFile = paste("CytoscapeInput-nodes-", paste(modules, collapse="-"), ".txt", sep=""),
                               weighted = TRUE,
                               threshold = 0.02,
                               nodeNames = modProbes,
                               altNodeNames = modGenes,
                               nodeAttr = moduleColors[inModule])

I tried different modules ,but the outcomes only had 19 genes, the lost one was always hub gene, I have no idea what to do next,someone can help me ?

r gene
• 1,846 views • link
written by yearn.nexus • yearn.nexus

whats your threshold?

• 0 views • link
written by 1769mkc 1769mkc

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