Issue reproducing TTN detection counts in In Silico Treatment Analysis
#579
by
LucasACyyy
- opened
Hi,
I’m reproducing the In Silico Treatment Analysis using the SCP1303 dataset. My cell type classification accuracy reached 0.8385, which aligns with your results.
However, I'm seeing a discrepancy in the perturbation step. I filtered the 29 training samples for disease == "NF" and cell_type == ["Cardiomyocyte_I", "Cardiomyocyte_II", "Cardiomyocyte_III"], resulting in 33,788 cells. While TTN is highly expressed across almost all these cells in my run, your reproduction table shows its n_detections at only around 10,000.
Did you apply additional quality control or specific filtering criteria for the cells used in this analysis?
Best,