Hi, this is a really cool method thank you guys for implementing it!
when dealing with multiple batches we'd usually align the GEX data using any batch correction method (scanorama, cca, harmony, etc...) then run the clustering on the SNN graph built from the corrected DimRed. there's no such a thing for citeseq (yet) although a number of preprints are tackling this now.
Since with citefuse we start with 2 distance matrices computed separately on the modalities, have you guys observed batch effects after joint-modality clustering, have you tested any other way of building a distance matrix from the GEX modality that is corrected for the batch covariate?
thank you.
fabiola
Hi, this is a really cool method thank you guys for implementing it!
when dealing with multiple batches we'd usually align the GEX data using any batch correction method (scanorama, cca, harmony, etc...) then run the clustering on the SNN graph built from the corrected DimRed. there's no such a thing for citeseq (yet) although a number of preprints are tackling this now.
Since with citefuse we start with 2 distance matrices computed separately on the modalities, have you guys observed batch effects after joint-modality clustering, have you tested any other way of building a distance matrix from the GEX modality that is corrected for the batch covariate? thank you. fabiola