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I was testing your tutorial on pseudobulk with pseudo replicates and I noticed that all the replicates created by your script are identical because you did not slice with the pseudo_rep slice that you created from the indices.
I propose you change this line:
from
`
for i, pseudo_rep in enumerate(indices):
rep_adata = sc.AnnData(X = samp_cell_subset.X.sum(axis = 0),
var = samp_cell_subset.var[[]])
`
to
rep_adata = sc.AnnData(X = samp_cell_subset[samp_cell_subset.obs_names.isin(pseudo_rep)].X.sum(axis = 0), var = samp_cell_subset.var[[]])
And thanks for the cool work you do :)
The text was updated successfully, but these errors were encountered:
Hi,
I was testing your tutorial on pseudobulk with pseudo replicates and I noticed that all the replicates created by your script are identical because you did not slice with the pseudo_rep slice that you created from the indices.
I propose you change this line:
from
`
for i, pseudo_rep in enumerate(indices):
`
to
rep_adata = sc.AnnData(X = samp_cell_subset[samp_cell_subset.obs_names.isin(pseudo_rep)].X.sum(axis = 0), var = samp_cell_subset.var[[]])
And thanks for the cool work you do :)
The text was updated successfully, but these errors were encountered: