About addGeneIntegrationMatrix() RNA cell assignments

[tzhu-bio]

Why the predictedGroup after prediction with RNA is not the same as the Object in RNA.

For example, cellA is Epithelial cell in RNAObject, but cellA is T cell in predictedGroup.

[rcorces]

I do not understand the question. If your ATAC-seq and RNA-seq data are acquired from different cells, then cellA does not exist in both objects

[tzhu-bio]

Sorry, I didn't describe the question clearly.

After addGeneIntegrationMatrix, ArchR will assign a RNA cell to each ATAC cell. predicteGroup represents the celltype in RNA and predictedCell is the cell name in RNA. I found that in RNA, cellA corresponds to T cell, but in the predictedCell cellA corresponds to Epithelial cell in the predicteGroup.

[rcorces]

In theory, this should not be possible. If you can create a reproducible example using the tutorial data, I'd be happy to take a look.

[abs51295]

@rcorces I am also facing a similar issue. I have multi-omic data and I analyzed RNA and ATAC separately. The overlap after processing both the modalities is ~50% and hence I use the integration method to label the remaining cells. As you can see in the image, the x axis is the predicted group and the y axis is the original label for the matched cells. So, what's celltype A in RNA gets celltype B in ATAC.

One possible reason: because these are all T-cell subclusters, the lineage between T cell subtypes is pretty hard to predict?

Another possible reason: I wasn't able to run the multiome workflow because of a known bug that's gonna be fixed in the next release. Hence, I relied on the GeneScoreMatrix computed by archR for integration.

Thanks

[rcorces]

@abs51295

One possible reason: because these are all T-cell subclusters, the lineage between T cell subtypes is pretty hard to predict?

Yes - I dont think GeneScores would be accurate enough for this

Another possible reason: I wasn't able to run the multiome workflow because of a known bug that's gonna be fixed in the next release.

I'm not sure exactly what you're referring to but I would encourage you to use the dev branch rather than wait for the next final release if you need that bug fix.