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gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration
MIT License
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Multiple batch variables #76

Closed sinkahak closed 1 year ago

sinkahak commented 1 year ago

Hi,

Thanks for an exciting software!

I was wondering if it was possible to use multiple data batches for batch correction in scglue.models.configure_dataset() ? My own efforts to do that have failed.

Best, Sini

Jeff1995 commented 1 year ago

Hi Sini! Thanks for your interest in GLUE!

GLUE does not support multiple batch covariates for now, but one way to make it work is to concatenate the different batch covariates. E.g., you may have two batch covariates like below:

Donor Sequencing run
d1 r1
d1 r2
d2 r1
d2 r2

You may concatenate them into one batch covariate:

Concatenated batch
d1-r1
d1-r2
d2-r1
d2-r2

Would that solve the problem?

sinkahak commented 1 year ago

Thanks, I will give that a try!