Hi, I'm analyzing scRNAseq data using the hdWGCNA package. I'm referring to the vignette created by the developer below ("hdWGCNA in single-cell data").

https://smorabit.github.io/hdWGCNA/index.html

I have 2 questions.

Q1. In the vignette, I'm not sure what 'hub gene signature scores' mean, which are calculated by ModuleExprScore() function with Seurat or UCell method. How are they different from MEs? Also, how can I find the obtained values?

Their example;

# compute gene scoring for the top 25 hub genes by kME for each module
# with UCell method
library(UCell)
seurat_obj <- ModuleExprScore(
  seurat_obj,
  n_genes = 25,
  method='UCell'
)
`

Q2. In seurat plotting functions, which data does DotPlot plot? It didn't look like it plotted ME values. Their example;

p <- DotPlot(seurat_obj, features=mods, group.by = 'cell_type')

Thank you for your help!

Yuko

The package (nor Seurat) is from Bioconductor, consider opening an issue at their GitHub.