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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Is metacell construction necessary? #280

Closed Tamalikaaa18 closed 1 week ago

Tamalikaaa18 commented 1 month ago

Hi Sam,

I have a dataset where the cells are of the same type but belong to different conditions and different samples. Is it necessary to create meta cells in this case? Can I skip this step and create the network using the single cell expression matrix? Will that work for me?

smorabit commented 1 month ago

We always recommend either creating metacells or using pseudobulk. In general single-cell data is too sparse to extract meaningful co-expression information, you can read more about this in our paper.

Tamalikaaa18 commented 1 month ago

Thank you so much for the advice. I ran the code and constructed meta cells for my data. However, the graph I achieved for the soft power threshold was a bit different. sp Can you please tell me what soft power should I take while constructing the co-expression networks?

smorabit commented 1 month ago

Unfortunately it looks like none of the soft power threshold values are acceptable based on this analysis. Essentially your data is too noisy. I can get a better idea of why this happened if you show me your previous code for processing your object and for hdWGCNA.

smorabit commented 1 week ago

Closing due to inactivity.