I am using WGCNA to identify the modules with co-expressed genes and assign these modules to traits.
When I generate a labeled heatmap (please see the code below) to check the module-trait correlation, I see some modules correlating with some traits. However, when I check the module membership vs. gene significance for the correlating modules and traits from the heatmap, there is no correlation (please see an example of the code I used below).
Could someone please explain the reason for getting different results? How should I interpret this result?
The code I used for the labeled heatmap:
labeledHeatmap(Matrix = moduleTraitCor, #xLabels = names(datTraits), xLabels = cond, #yLabels = names(MEs), yLabels =namey, #ySymbols = names(MEs), ySymbols = namey, colorLabels = FALSE, colors = blueWhiteRed(50), textMatrix = textMatrix, setStdMargins = FALSE, cex.text = 0.9, zlim = c(-1,1))
The code I used for the module membership (MM) vs. gene significance (GS) plot creation:
verboseScatterplot(abs(geneModuleMembership[moduleGenes, column]), abs(geneTraitSignificance[moduleGenes, 1]), xlab = paste("Module Membership in", module, "module"), ylab = "Gene significance for fat", main = paste("Module membership vs. gene significance\n"), cex.main = 1.2, cex.lab = 1.2, cex.axis = 1.2, col = module)