Question: WGCNA Different Module Results
0
gravatar for ninabhatia3
14 months ago by
ninabhatia30 wrote:

I'm using WGCNA to find gene modules- I've been using both the code from http://pklab.med.harvard.edu/scw2014/WGCNA.html and from here https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/ and I am getting different results in the number of modules/module sizes. Can anyone explain these discrepancies.

rna-seq R • 790 views
ADD COMMENTlink modified 14 months ago by Sam3.2k • written 14 months ago by ninabhatia30
1
gravatar for Sam
14 months ago by
Sam3.2k
New York
Sam3.2k wrote:

One of the step of WGCNA involves hierachical clustering, which is partially random. Unless you've set the random seed before each run, you'd expect to see slight difference in the number of modules, module size and module membership, especially when your sample size is relatively small

ADD COMMENTlink written 14 months ago by Sam3.2k

Thank you so much!

Do you know why the Hovarth code uses this command : dynamicMods = cutreeDynamic(dendro = geneTree, distM = dissTOM, method="hybrid", deepSplit = 2, pamRespectsDendro = FALSE, minClusterSize = minModuleSize); when creating modules stepwise as opposed to this command used in the Harvard version: dynamicMods = cutreeDynamic(dendro = geneTree, method="tree", minClusterSize = minModuleSize);

I ask because using the different commands gives me a vastly different amounts of modules.

ADD REPLYlink written 14 months ago by ninabhatia30

I'm not sure. But from the glance of it, those two codes are using two different method (tree vs hybrid). So I am not surprise that they generate a different result

ADD REPLYlink written 14 months ago by Sam3.2k
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: 1227 users visited in the last hour