The tutorial for scType indicates to use the scale.data slot of the RNA assay. Is this still the case if I am using a SCTransformed and integrated dataset?
Also, does the scale.data need to include all genes, or can it be just those that are most variable (default for SCT assay)? I ask because scale.data is not a sparse matrix and thus is quite large if all genes are included for my dataset.
Hello,
The tutorial for scType indicates to use the scale.data slot of the RNA assay. Is this still the case if I am using a SCTransformed and integrated dataset?
Also, does the scale.data need to include all genes, or can it be just those that are most variable (default for SCT assay)? I ask because scale.data is not a sparse matrix and thus is quite large if all genes are included for my dataset.
Thank you for the help!