User: harelarik

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Posts by harelarik

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Comment: C: WGCNA export to cytoscape
... Thank you very much! ...
written 6 weeks 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 weeks ago by harelarik0
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Comment: C: WGCNA export to cytoscape
... Thank you very much! ...
written 6 weeks ago by harelarik0
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Comment: C: How to select mergeCutHeight in WGCNA?
... Thank you! ...
written 6 weeks 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 weeks 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 7 weeks ago by harelarik0 • updated 6 weeks ago by Peter Langfelder1.4k
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Comment: C: How to extract the voom normalized value for each observation?
... Dear Gordon, Thank you very much! ...
written 11 weeks 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 11 weeks ago by harelarik0
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Comment: C: How to extract the voom normalized value for each observation?
... Thank you! ...
written 11 weeks ago by harelarik0
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Comment: C: How to extract the voom normalized value for each observation?
... Thank you very much. I. Are the $E values are "logCpm+0.5" transformation of raw counts or the of  TMM values (made by calcNormFactors(y))?   II. Considering one found Differentially expressed genes, based on  voom values, and would like to continue to downstream analysis (e.g., network analysis) ...
written 11 weeks ago by harelarik0

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