Question: (Closed) Module membership vs gene significance does not correlate (WGCNA)
0
Neberirni • 0 wrote:
Hi,
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?
Thanks!
The code I used for 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 vs. gene significance 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)
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modified 16 months ago
by
Istvan Albert ♦♦ 84k
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written
16 months ago by
Neberirni • 0
The WGCNA developer is not active on Biostars. He is more active on the Bioconductor forum, even though WGCNA is not a Bioconductor package - it is a CRAN package. Really, the answer should come from him.
One thing that I notice is that, in verboseScatterplot, you are using absolute values.
...and you went to Bioconductor to post it: https://support.bioconductor.org/p/119159/
Cross-posted on Bioconductor: https://support.bioconductor.org/p/119159/
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.