User: harelarik
harelarik • 10
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Posts by harelarik
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... I was advised that it is possible to use modulePreservation with a single data set. Single set can be supplied both as reference, and as a test set. I the results, one should focus on module quality.
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written 20 months ago by
harelarik • 10
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... Hi,
I am studying only one co-expression network utilizing WGCNA.
I would like to validate that the modules identified by WGCNA are significantly above randomly generated modules.
1. What would be the best way to do it?
2. Is there a way to utilize the modulePreservation function to study ...
written 20 months ago by
harelarik • 10
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C: WGCNA export to cytoscape
... Thank you very much!
...
written 23 months ago by
harelarik • 10
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C: WGCNA export to cytoscape
... Would be a good way to select the "threshold", when using exportNetworkToCytoscape?
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written 23 months ago by
harelarik • 10
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C: WGCNA export to cytoscape
... Thank you very much!
...
written 23 months ago by
harelarik • 10
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C: WGCNA export to cytoscape
... 1. So the "weight" output of the edges file generated by exportNetworkToCytoscape is based on Topological Overlap Matrix (TOM), as oppesd to pearson correlation used to calculate distance from eigengene during modules generation which can be restricted by minKMEtoStay? Is it correct?
2. IS this ...
written 23 months ago by
harelarik • 10
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... Hi,
What is would be a good way to select mergeCutHeight for modules generation with blockwiseModules?
Thank you,
Arik
...
written 23 months ago by
harelarik • 10
• updated
23 months ago by
Peter Langfelder • 2.3k
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... Dear Gordon, Thank you very much!
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written 2.0 years ago by
harelarik • 10
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... Thank you!
Would you recommend using logCPM on raw counts on or TMM transformed values?
...
written 2.0 years ago by
harelarik • 10
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