I’d like to reuse this dataset https://ftp.ncbi.nlm.nih.gov/geo/series/GSE120nnn/GSE120575/suppl/GSE120575_Sade_Feldman_melanoma_single_cells_TPM_GEO.txt.gz for test some hypothesis.
The technology used is SMART-Seq2 and the matrix is already trasformed in TPM.
I have two question:
- Do you have some suggesting how to import in scanpy and avoid a further normalization step?
- My idea is to check the expression of gene in this human patients that is generally low expressed, MAGIC could be a good strategy?