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Question: WGCNA - module membership via max kME?
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gravatar for ly.leifels
11 days ago by
ly.leifels0
ly.leifels0 wrote:

Hello,

I am working with a scRNA-seq dataset and I want to analyse module memberships for low abundance genes via WGCNA generated gene co-expression networks. I found that the module-color assignments from BlockWiseModules() are different from the module it would be assigned to looking only at the maximum abs(kME) value from singnedkME(). I am computing the kME-Table for all modules based on the module eigengenes generated from BlockWiseModules(). The color-assignment is important to me, for visualisation of switching modules during downscaling. Looking at the maximum kME-value for a gene it gets assigned to, for example, the black-module, while the module assignment from BlockWiseModules$colors says it is assigned to the grey-module. There is a analyses step mentioned in the supplementary material of the WGCNA-paper, saying that after merging close modules genes with higher kME-values for another module than the one they are assigned to get switched to the higher correlated module. How can this difference still happen? How are genes assigned to modules in detail? Thank you for any hints!! 

 

 

 

 

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