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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Question about Module Eigengene Loadings #262

Open ofarrelle opened 2 weeks ago

ofarrelle commented 2 weeks ago

My interpretation of module eigengenes is that each module gets a unique eigengene, which describes the "direction" of the module in the high dimensional gene-space. And that each eigengene is defined as a linear combination of the genes (whose coefficients are "loadings")

When I run GetMELoadings it only returns one vector of values, even though my analysis has 8 modules. Is my interpretation of an eigengene and its loadings correct? I would have expected 8 sets of loadings, one for each module.

Thank you for providing this package!

smorabit commented 1 week ago

Module eigengenes are obtained by performing PCA on a gene expression matrix containing the genes for that particular module, and then taking PC1. We only report the loadings for PC1, not the loadings for the other PCs.