Can I use RPCA in FindTransferAnchors between RNA and ATAC?

[plbngl]

Hello,
I am following the vignette for label transfer from a RNA reference to an ATAC query but the datasets are very large (500kcells x 5k hvg for rna and 250kce,,s x 5k hvg for atac) and there are memory issues ( tried with 1.5 tera) and wondering if using the RPCA reduction instead of CCA would be still appropriate although it was not the recommended choice for RNA to ATAC.

Thank you!
Paola

[timoast]

Generally we find that CCA has better performance for cross-modality integration, but you could certainly try other approaches and see how it performs on your data

Other alternatives for cross-modality integration would be methods like bridge integration (https://www.nature.com/articles/s41587-023-01767-y) or StabMap (https://www.nature.com/articles/s41587-023-01766-z)