Hello, I am interested in performing differential-expression analysis between cell-types on the following dataset:
I already downloaded the well annotated dataset containing assigned celltypes.
My plan was to use the scran package for normalization of raw counts. One step in the pipeline is to pool samples by the "quickCluster"-function in order to obtain cell-types. However, as I said, I already have the celltype information from the authors. If I compare the annotated cell-types to the clusters obtained by "quick-cluster" I see the same amount of clusters, but the cluster-composition is totally different.
How would you proceed in this case?