The use of Co-embedding function

Question

The use of Co-embedding function

LalicJ opened this issue a year ago · 2 comments

Hi, sorry to bother you. When I run Co-embedding(), I have a question. If I don't ran harmony or other methods on snRNA-seq and snATAC-seq datasets for removing batch effect, what weight.reduction value should I use?

Do you have any suggestions? Any help would be greatly appreciated.

Answer 1 · 2023-05-22T20:56:59.000Z

Hi,

You can set weight.reduction as the dimension name used in snATAC-seq, such as LSI,
because here we aim to first transfer the gene expression profile from snRNA-seq to snATAC-seq.

Best,
Zhijian

Answer 2 · 2023-05-23T01:56:09.000Z

Thanks! I'll try it.