Hi,
I got the 0 probability when I showed ‘pvals_adj’.
Is this what you expected?
The code is as follows.
stat = 't-test'
sc.tl.rank_genes_groups(data, 'class', method=stat, key_added = stat, corr_stat='bonferroni')
pvals = pd.DataFrame(data.uns[stat]['pvals_adj'])
| 16011 | 0.000000e+00 | 5.122659e-117 | 0.000000e+00 | 0.0 | 1.167093e-191 | 3.454282e-141 | 3.048517e-121 | 7.394720e-83 | 0.000000e+00 |
|---|---|---|---|---|---|---|---|---|---|
| 16012 | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | 0.0 | 1.343815e-242 | 2.026553e-249 | 3.782163e-140 | 2.896768e-157 | 0.000000e+00 |
| 16013 | 0.000000e+00 | 0.000000e+00 | 0.000000e+00 | 0.0 | 0.000000e+00 | 7.201276e-143 | 1.552978e-173 | 1.837665e-77 | 1.071093e-131 |
| 16014 | 0.000000e+00 | 4.389539e-163 | 0.000000e+00 | 0.0 | 6.732805e-237 | 2.432724e-180 | 1.248841e-220 | 2.773689e-73 | 0.000000e+00 |
| 16015 | 0.000000e+00 | 1.156094e-318 | 0.000000e+00 | 0.0 | 0.000000e+00 | 5.938224e-181 | 1.930398e-135 | 1.805501e-72 | 0.000000e+00 |