Question: Threshold in WGCNA
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gravatar for Arindam Ghosh
14 months ago by
Arindam Ghosh340
Finland
Arindam Ghosh340 wrote:

In WGCNA there are 3 major steps:

  1. Correlation calculation between genes
  2. Adjacency matrix generation by raising correlation matrix to power β (soft threshold)
  3. TOM based dissimilarity matrix generation for identifying modules/clusters

If I understand correctly, β is selected such that the resulting network fits scale-free topology. Till step 2, we will have all-to-all connection between the genes. The adjacency matrix in step 2 gives for the weight for each edge. At this stage how does it select which edges to retain in the final network?

rna-seq wgcna • 550 views
ADD COMMENTlink written 14 months ago by Arindam Ghosh340
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gravatar for andres.firrincieli
14 months ago by
andres.firrincieli1.1k wrote:

The adjacency matrix in step 2 gives for the weight for each edge. At this stage how does it select which edges to retain in the final network?

In WGCNA you do not select which edges must be retained in the final network. However, when you raise the correlation matrix to power β you are suppressing edges with low correlations values: link

edit: There is a way to filter out genes with low connectivity Check the SI of this paper

ADD COMMENTlink modified 14 months ago • written 14 months ago by andres.firrincieli1.1k
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