DissTOM and Cytoscape - WGCNA
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Entering edit mode
20 months ago

Hi,

In the WGCNA why we want to calculate de dissimilarity TOM? The other question that I have is, once that I have my network visualization with the igraph package how I can export it to cytoscape? Which steps I should follow?

Thanks,

Silvia

wgcna dissTOM cytoscape • 859 views
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Entering edit mode
20 months ago
scooter ▴ 470

Hi Silvia, WGCNA uses the dissimilarity matrix from the topological overlap matrix to reduce the effects of noise and spurious associations (from the manual), before doing the hierarchical clustering.

As to your second question, probably the easiest way to get from igraph in R to Cytoscape is to use the RCy3 package, which includes specific functions that will talk to the running cytoscape and push the igraph network to it.  You can read more about RCy3 at https://github.com/cytoscape/cytoscape-automation/wiki


-- scooter

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Entering edit mode

Ok, thank you! And it’s the same reason for when we do the dissimilarity of eigengenes coexpression [MEDiss = 1-cor(MEs)]?

Silvia