You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
In [23]: scalesc = ssc.ScaleSC(data_dir=data_dir,
...: max_cell_batch=1e5, # no more than 1e5 is suggested
...: preload_on_cpu=True,
...: preload_on_gpu=True,
...: save_raw_counts=False,
...: save_norm_counts=False,
...: output_dir='test_scalesc_2.9M_results')
In [24]:
In [24]: print(scalesc.adata.shape)
(2915977, 5001)
In [25]: print(scalesc.reader.shape)
(-1, -1)
scalesc.reader.shape displays (-1, -1), which is very strange, causing problems in subsequent data processing. I implore you to help. Thank you!
Hi kunkun, have you setup any cell or gene filters? I would recommend to set filters to both cell and gene as described in tutorial and try it again. You can set min_count=0 If you don't really need it.
Just let me know if it doesn't work.
Activity
haotianzh commentedon Mar 1, 2026
Hi kunkun, have you setup any cell or gene filters? I would recommend to set filters to both cell and gene as described in tutorial and try it again. You can set
min_count=0If you don't really need it.Just let me know if it doesn't work.