trying to estimate the relative prevalence of particular cell types (clusters) in a given brain region. I have downloaded the cluster ID’s and can look them up in Supplemental Table 7 in Yao (or cl.df.CCN202307220). Would the best columns to use be v3.size & v2.size (perhaps a sum)?
As we didn’t profile many regions in 10X v2, it’s the best to use v3.size. However, even in 10x v3, we didn’t have even sampling of all the areas. The estimate should be quite reasonable within each class. You can also check the cell number based on MERFISH