I was wondering whether it makes sense (or even possible) to use the SC3-scater packages to analyse bulk-RNA. We have a data set from human cancer with ~350 samples. In those I have three risk groups and multiple abnormalities within, which I would like to use like with scRNA as cell types and sub-types.
As I don't have Spike-Ins in the dataset, I was thinking either to use the normalised values from a previous DESeq2 analysis i did or normalise with the size factors by calculating the geometric mean.
I would appreciate any Ideas