Findtransferanchors() and SCT

[michaelhojungyoon]

There's been a few posts about this recently, but it is still very confusing on what is appropriate.

Essentially, I have an SCTransform() integrated rpca object and a reference object that also underwent SCTransform() in pca space and I wanted to transfer labels from the reference to the query using:

anchors <- FindTransferAnchors(reference = reference.object,
query = x,
dims = 1:30,
reference.reduction = "pca",
normalization.method = "SCT",
recompute.residuals = FALSE,
reference.assay = "SCT",
query.assay = "SCT",
verbose = TRUE)

From my understanding, it makes sense to keep the reference and query as SCT, but I'm confused on why some others say you can keep the query as RNA and recompute.residuals = TRUE.