Question: (Closed) Module membership vs gene significance does not correlate (WGCNA)
0
gravatar for Neberirni
16 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 16 months ago by Istvan Albert ♦♦ 84k • written 16 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 16 months ago by Kevin Blighe61k

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

ADD REPLYlink written 16 months ago by Kevin Blighe61k

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 16 months ago • written 16 months ago by Kevin Blighe61k
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