Question: WGCNA Different Module Results
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gravatar for ninabhatia3
7 weeks 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 • 147 views
ADD COMMENTlink modified 7 weeks ago by Sam2.4k • written 7 weeks ago by ninabhatia30
0
gravatar for Sam
7 weeks ago by
Sam2.4k
New York
Sam2.4k 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 7 weeks ago by Sam2.4k

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 6 weeks 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 6 weeks ago by Sam2.4k
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