Open ConDem94 opened 1 year ago
Hi Constantinos
One way of doing this is to use the limma removeBatchEffect
function. What I would do is get the transformed proportions by running the getTransformedProps function in speckle:
props <- getTransformedProps(sce$cluster, sce$sample, transform="logit")
and then passing the transformed proportions to removeBatchEffect
props.nobatch <- limma::removeBatchEffect(props$TransformedProps, batch=batch, design=design)
Have a read of the help for the removeBatchEffect function. The design matrix should include the covariates of interest, and exclude the batch variable.
?limma::removeBatchEffect
Then you could cluster props.nobatch
.
Hope that helps.
Cheers, Belinda
Is it possible to obtain batch normalized proportions using the propeller package? I have multiple samples from 5 different studies which are integrated using scvi. I would like to perform de novo clustering based on the proportions of 50-60 cell types. Is it possible to retrieve transformed proportions by regressing out the batch effects from the studies?
Thank you!
Best wishes, Constantinos