Hi, I don't have any experience in R and am running a WGCNA on my RNA-Seq time-course data. I got everything working thanks to the tutorials on female mice. However, I cannot get the network visualisation in R working, and also the export to cytoscape. I will address these each in order.

First, I have tried using the following code from the tutorial:

dissTOM = 1-TOMsimilarityFromExpr(datExpr, power = 6);
# Transform dissTOM with a power to make moderately strong connections more visible in the heatmap
plotTOM = dissTOM^7;
# Set diagonal to NA for a nicer plot
diag(plotTOM) = NA;
# Call the plot function
sizeGrWindow(9,9)
TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes")

I get: Error in x[, iy] : subscript out of bounds

I also tried:

TOM.mat = as.matrix(TOM)
dissTOM = 1-TOM.mat
# Transform dissTOM with a power to make moderately strong connections more visible in the heatmap
plotTOM = dissTOM^7;
# Set diagonal to NA for a nicer plot
diag(plotTOM) = NA;
# Call the plot function
sizeGrWindow(9,9)
TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes")

I get: Error in TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes") : ERROR: number of color labels does not equal number of nodes in dissim. nNodes != dim(dissim)[[1]]

Secondly, regarding the export to cytoscape, I have tried numerous code that I obtained from the tutorial and the forum posts, such as:

# Select modules
modules = c("turquoise");

# Select module probes
probes = colnames(datExpr)
inModule = (moduleColors==module);
modProbes = probes[inModule];

# Recalculate intramodular connectivity (IMConn)
IMConn = softConnectivity(datExpr[, modProbes]);

# Select the corresponding Topological Overlap
length(inModule)
modTOM = dissTOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)
cyt = exportNetworkToCytoscape(modTOM,
                               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,
                               nodeAttr = moduleColors[inModule])

AND

module = "blue"
datexpr_green = datExpr[,moduleColors == module]
TOM_green = TOMsimilarityFromExpr(datexpr_green, power = 3, networkType = "signed", TOMType="signed Nowick");
probes = names(datexpr_green)
dimnames(TOM_green) = list(probes, probes)
nTop = 30;
IMConn = softConnectivity(datExpr[, modProbes]);
top = (rank(-IMConn) <= nTop)
cyt = exportNetworkToCytoscape(TOM_green[top, top],
                               edgeFile = paste("CytoscapeInput-edges-", paste(module, collapse="-"), ".txt", sep=""),
                               nodeFile = paste("CytoscapeInput-nodes-", paste(module, collapse="-"), ".txt", sep=""),
                               weighted = TRUE,
                               threshold = 0.02,
                               nodeNames = probes,
                               altNodeNames = probes);

The aforementioned export code produces a text file with no data, only column names. Some of my interesting modules are quite large, hence I would like to restict the cytoscape output to the top X hub genes only.

If someone could please help me get to the bottom of what is going wrong, that would be immensely appreciated.

As mentioned, I can generate the geneInfo files and module-trait relationships just fine, but the network and eigengene plots are beyond my skills. I have re-run the entire code from scratch multiple times.

Thank you, Gianni