Clarification on choosing a reference and SCTransform. about scalign HOT 2 CLOSED

Hi,

The reference data set is chosen based on the 'reference.data' argument to scAlignMulti(). Assuming the list of SCE objects is named before calling scAlignCreateObject() then setting reference.data to one of those names will specify the reference set, otherwise all-pairs alignment is performed.

We haven't tried SCTransform as a normalization method but using the residuals from SCTransform should work as well if not better than the results of ScaleData.

from scalign.

Alright that worked.
Also the tutorials for multiway alignment has an error in it, I believe. When your extracting the common set of variable genes across datasets, and then pull those rows to create the SCE object it throws on out of bounds error. I fixed this by intersecting the union with all genes in all batches.

Thanks.

from scalign.