search

smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
Other
315 stars 31 forks source link

Using normalized count for MetacellsByGroups #260

Open jeji0209 opened 1 week ago

jeji0209 commented 1 week ago

Hello. Thank you for developing this useful package.

My question is, is it acceptable to use normalized counts, that is, the 'data' layer (my Seurat object is v5) for the MetacellsByGroups function? My situation is that I have a Seurat object that is comprised of multiple publicly available datasets, and one of the data did not provide their raw count, so I only have their normalized counts. Therefore, I am afraid it might be inaccurate to use the 'counts' layer to build metacells.

Also, my following question is that if I use normalized counts to build meta cells, would it still be necessary to run the NormalizeMetacells function?

Thank you in advance :)

smorabit commented 1 week ago

In general, yes we do allow the user to select a specific slot/layer to use for MetacellsByGroups. However I strongly recommend using the raw counts and not the normalized data slot/layer. For your case I would recommend removing the dataset that did not have raw counts prior to running hdWGCNA, or you can request the original authors to provide you with the counts matrix.