Question: Confusion about WGCNA results
0
gravatar for younglin113
10 weeks ago by
younglin11350
younglin11350 wrote:

Lately, I have tried to perform WGCNA analysis in R with WGCNA package against a RNA-seq dataset. And in this process, I found the numbers of color modules displayed by labeledHeatmap and Epigegene Network were different. And the code that produced those two plots are:

labeledHeatmap(Matrix = moduleTraitCor,
           xLabels = colnames(design),
           yLabels = names(MEs),
           ySymbols = names(MEs),
           colorLabels = FALSE,
           colors = greenWhiteRed(50),
           textMatrix = textMatrix,
           setStdMargins = FALSE,
           cex.text = 0.5,
           zlim = c(-1,1),
           main = paste("Module-trait relationships"))


plotEigengeneNetworks(MET, "",
                      marDendro = c(0,4,1,2),
                      marHeatmap = c(3,4,1,2),
                      cex.lab = 0.8, xLabelsAngle = 90)

The plots I got are as following:

labeledHeatmap

Epigengene Network

As you can see, there are 32 modules in labeledHeatmap and only 31 in Epigengene Network. So, what's the secret here or did I miss something? Thanks for your time!!

software error • 188 views
ADD COMMENTlink modified 10 weeks ago by andres.firrincieli1.1k • written 10 weeks ago by younglin11350

enter image description here

ADD REPLYlink written 10 weeks ago by younglin11350
0
gravatar for andres.firrincieli
10 weeks ago by
andres.firrincieli1.1k wrote:

By default the function plotEigengeneNetworks exclude the grey module which include non-module genes

ADD COMMENTlink written 10 weeks ago by andres.firrincieli1.1k

Thanks a lot for your response. It helps a lot. But according to the labeledHeatmap, the "grey" module correlated to the AD trait most closely, should I ignore this and focus on "yellow" module for further analysis?

ADD REPLYlink written 10 weeks ago by younglin11350

See my answer here

Since the clustering algorithm is not perfect, my guess is that the hub of the grey module could actually belong to the yellow module. How many genes do you have in the grey module? What is the output of 1-cor(MEs)?

ADD REPLYlink written 10 weeks ago by andres.firrincieli1.1k

There are 1564 genes in the "yellow" module. And the 1-cor(MEs) result between MEgrey and MEyellow is 0.2207696.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by younglin11350

the dissimilarity is quite low. My suggestion is to merge the modules whose expression profile is very similar (2.b.5)

ADD REPLYlink written 9 weeks ago by andres.firrincieli1.1k

I got that. Thanks a lot for your suggestion.

ADD REPLYlink written 9 weeks ago by younglin11350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1676 users visited in the last hour
_