Question: (Closed) Module membership vs gene significance does not correlate (WGCNA)
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gravatar for Neberirni
5 months ago by
Neberirni0
Neberirni0 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)
ADD COMMENTlink modified 5 months ago by Istvan Albert ♦♦ 81k • written 5 months ago by Neberirni0
1

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.

ADD REPLYlink written 5 months ago by Kevin Blighe46k

...and you went to Bioconductor to post it: https://support.bioconductor.org/p/119159/

ADD REPLYlink written 5 months ago by Kevin Blighe46k

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by Kevin Blighe46k
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