Hello,

My TOM file is empty. It just shows NA, NA, NA, NA, NA

I am trying to export network to VisANT and Cytoscape, following instructions in the online tutorial.

The code I used is:

#PART 5 - Export to External
# Recalculate topological overlap
TOM = TOMsimilarityFromExpr(datExpr, power = 3);
# Read in the annotation file
annot = read.csv(file = "Gene Annotation.csv");
# Select module
module = "brown";
# Select module probes
probes = names(datExpr)
inModule = (moduleColors==module);
modProbes = probes[inModule];
# Select the corresponding Topological Overlap
modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
# Export the network into an edge list file VisANT can read
vis = exportNetworkToVisANT(modTOM,
                            file = paste("VisANTInput-", module, ".txt", sep=""),
                            weighted = TRUE,
                            threshold = 0,

The output file contains no data.

What is happening?

Thank you, Gianni