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Question: Intramodular connectivity RNA-seq WGCNA
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gravatar for adriana.gallego.02
13 months ago by
adriana.gallego.020 wrote:

Cordial greeting

Someone could help me with the script to calculate intramodular connectivity for RNA-seq data?

This is the code that I have so far, is this correct?

module = c("indianred4");

# Select module probes
probes = colnames(datExpr)
inModule = (moduleColors==module);
modProbes = probes[inModule]; 
# Recalculate intramodular connectivity (IMConn)
IMConn = softConnectivity(datExpr[, modProbes]);

# Select the corresponding Topological Overlap
length(inModule)
modTOM = TOM[inModule, inModule];
dimnames(modTOM) = list(modProbes, modProbes)

TOM.mat = as.matrix(mod)

Thanks

ADD COMMENTlink modified 13 months ago by Peter Langfelder1.5k • written 13 months ago by adriana.gallego.020
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gravatar for Peter Langfelder
13 months ago by
United States
Peter Langfelder1.5k wrote:

The code should work. RNA-seq, after suitable normalization and transformation, can be analyzed just any other data. You may want to look at the WGCNA FAQ, especially point 4. Then simply follow the WGCNA tutorials or the code in the book (which you seem to be following already).
 

ADD COMMENTlink written 13 months ago by Peter Langfelder1.5k

Thanks Dr. Langfelder, I have one last question, how can I visualize this intramodular connectivity, for example using Cytoscape?

Thanks

ADD REPLYlink written 13 months ago by adriana.gallego.020
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