Hello everyone,
I am working on a single-cell dataset and have performed DEG analysis to identify the cell types most affected by a disease condition. Recently, I became familiar with hdWGCNA and thought it might be a better approach or complementary one as it consider genes interconnectedness. Consequently, I applied WGCNA to the highly affected genes identified in the DEG analysis. However, I have some questions:
Does it make sense to focus on the vulnerable cell types identified through DEG analysis and build a co-expression network for these specific cell types (e.g to do hdWGCNA based on DEG results)? Would I obtain the same results if I used hdWGCNA independently?
When I did my DEG analysis I regressed out sex, PMI, and batch. Not sure if regressing same variables (not using harmony) will be the best to keep the consistencies between these two.
Do you recommend any specific approach for incorporating hdWGCNA into my analysis?
I would greatly appreciate any input!
Thank you, Paria
hello, I don't have an answer but I would be interested to know if you found a solution for your problem because it would be also of iterest for me, let me know!