User: harelarik

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harelarik0
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Posts by harelarik

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Comment: C: Study Modules significance (or Modules Preservation) in ONE network
... 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. ...
written 3 months ago by harelarik0
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Study Modules significance (or Modules Preservation) in ONE network
... 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 ...
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Comment: C: WGCNA export to cytoscape
... Thank you very much! ...
written 6 months ago by harelarik0
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Comment: C: WGCNA export to cytoscape
... Would be a good way to select the  "threshold", when using exportNetworkToCytoscape? ...
written 6 months ago by harelarik0
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Comment: C: WGCNA export to cytoscape
... Thank you very much! ...
written 6 months ago by harelarik0
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Comment: C: How to select mergeCutHeight in WGCNA?
... Thank you! ...
written 6 months ago by harelarik0
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Comment: 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 6 months ago by harelarik0
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How to select mergeCutHeight in WGCNA?
... Hi,   What is would be a good way to select mergeCutHeight for modules generation with  blockwiseModules?       Thank you,   Arik   ...
wgcna mergecutheight written 6 months ago by harelarik0 • updated 6 months ago by Peter Langfelder1.5k
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Comment: C: How to extract the voom normalized value for each observation?
... Dear Gordon, Thank you very much! ...
written 7 months ago by harelarik0
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Comment: C: How to extract the voom normalized value for each observation?
... Thank you!   Would you recommend using logCPM on raw counts on or TMM transformed values? ...
written 7 months ago by harelarik0

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