User: bioming

gravatar for bioming
bioming10
Reputation:
10
Status:
New User
Location:
Queen's University
Last seen:
8 months, 3 weeks ago
Joined:
10 months ago
Email:
r*******@gmail.com

Bioinformatics MSc student at Queen's University School of Computing. Method development for genome wide epistasis analysis.

Posts by bioming

<prev • 5 results • page 1 of 1 • next >
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Comment: C: WGCNA gene clusters vs eigengenes
... Thank-you for the thorough explanation, it makes sense now. ...
written 10 months ago by bioming10
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Comment: C: WGCNA gene clusters vs eigengenes
... Ohhhh sorry I can't believe I miss that, so you get the 1stPC from the modules identified from hclust(as.dist(dissTOM) ? ...
written 10 months ago by bioming10
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Comment: C: WGCNA gene clusters vs eigengenes
... Thank-you so much for your answer, just to double check if I understood correctly: geneTree = hclust(as.dist(dissTOM), method = "average") is clustering genes into modules - using gene-gene cor values vs. METree = hclust(as.dist(MEDiss), method = "average") which is clustering modules - u ...
written 10 months ago by bioming10
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how is the topological overlap (TOM) algorithm calculated?
... Hello, I'm exploring the WGCNA package and am trying to understanding the math behind calculating values in a topological overlap matrix (TOM). I understand the purpose of TOM is to better estimate "connectedness" of 2 nodes/genes than merely correlation from the similarity matrix. I was reading thr ...
tom network analysis topological overlap matrix written 10 months ago by bioming10 • updated 7 months ago by udi.landau20
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WGCNA gene clusters vs eigengenes
... Hello, I'm trying to go through the WGCNA tutorial on mice liver data from https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/. I understood the concepts from expression matrix -> soft thresholding -> adjacency matrix -> dissTOM -> hclust. This is where ...
wgcna eigengenes hclust network analysis written 10 months ago by bioming10 • updated 10 months ago by finswimmer13k

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