I have scRNA data in a form of a
SingleCellExperiment object that I previously filtered, normalised, clustered, with genes selected.
scmap vignette, I created a
SingleCellExperiment object out of the HPCA dataset, selected features and created indexes.
I am now ready to project my scRNA data into these indexes.
However, is it correct to project scRNA read counts (or CPM) on HPCA reference indexes knowing that HPCA came from affymetrix data normalized differently (HPCA values are robust multi-array average (RMA) expression measure)?