Using Harmony with Multi-Ome

[waltno]

I am wondering what is the best way to use Harmony to correct batch effects with multi-ome data. Should I add harmony for both ATAC/RNA assays and Harmony again with combined dimensions? Or run harmony at the very end?

[rcorces]

I'm not sure there is a "right" answer to this. I dont think I would run Harmony 3 times (both atac/rna and again for combined). I think I would either run it once for both ATAC and RNA prior to making the combined dims or just once after making the combined dims.

[sylestiel]

@rcorces

When working with multiple multiome datasets, if I choose to run Harmony after the step
proj <- addCombinedDims(proj, reducedDims = c("LSI_ATAC", "LSI_RNA"), name = "LSI_Combined")

1. How can I generate/render Harmony based embedding using LSI_ATAC and LSI_RNA in addition

2. How do I specify getMarkerFeatures based on Harmony correction?