Paired Multiome samples

[icenzano]

Discussed in #2141

^{Originally posted by icenzano March 28, 2024}
Hello everyone! I am starting with multi-omics analysis and I need to analyze our three 10x multi-omics datasets with ArchR. However, I am not sure about the correct order to follow. If I have multiple samples, which is the correct approach?

1. Should I integrate RNA samples and ATAC samples separately using Harmony (or any other batch correction method) and then combine/integrate both omics layers using the batch corrected dimension coming from each omic?
2. Or, should I integrate both omics layers first and then correct the batch effect coming from having three samples using Harmony (or any other batch correction method) within the combined dimension?
   Thank you.

[rcorces]

Hi @icenzano! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.