Hi All

I'm using WGCNA to look at some large RNAseq datasets. I'd like to plot a map of the structure of the whole network in Cytoscape using the relationships between the modules/module eigengenes to produce the network. The function

```# Recalculate module eigengenes MEs = moduleEigengenes(datExpr, moduleColors)$eigengenes

Plot the relationships among the eigengenes and the trait

sizeGrWindow(5,7.5); par(cex = 0.9)

plotEigengeneNetworks(MEs, "Eigengene Adjacency Heatmap", marHeatmap = c(3,4,2,2),

• plotDendrograms = FALSE, xLabelsAngle = 90, printAdjacency = TRUE, cex.adjacency = 0.9) ```

allows me to generate a heatmap mapping the adjacency between module eigengenes with the adjacency values plotted on the map, but I have been unable to work out how to get those numerical values exported into a csv file so I can use them to construct the network.

I have searched everywhere for an answer and not found anything so if anyone can help that would be great... I'm not experienced with WGCNA/R and I'm struggling a bit so I have far too many questions:.

1) Am I right in thinking I can construct a rational map of the network using these values?
2) How do I get the values out of the program?
3) How to I get the correlation values and should I be using those instead?
4) Can I export the eigengene network directly to cytoscape?

If anyone can help it would be most appreciated!

Hannah