diff_exp not working after updating wot #72
Comments
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What version of anndata do you have? Thanks.
…On Thu, Oct 24, 2019 at 3:18 PM rosshandler ***@***.***> wrote:
Hi WOT developers,
I am experiencing some problems with diff_exp after updating wot. I am
able to compute the transport maps and the fates matrices but I now get an
error regarding data dimensions that I think is related to changes in the
anndata object but I just don't know how to fix.
The error message is:
9 days
BP1 vs BP2, day 6.5, day 6.5
Trying to set attribute .X of view, making a copy.
Traceback (most recent call last):
File "/homes/iimaz/miniconda3/bin/wot", line 8, in
sys.exit(main())
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/*main*.py",
line 23, in main
cmd.main(args)
File
"/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/commands/diff_exp.py",
line 71, in main
compare=compare, delta_days=delta_days)
File
"/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/tmap/diff_exp.py",
line 77, in diff_exp
features=features)
File
"/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/tmap/diff_exp.py",
line 114, in __do_comparison
scores[np.isnan(scores)] = 0
File
"/homes/iimaz/miniconda3/lib/python3.6/site-packages/anndata/core/views.py",
line 29, in *setitem*
container[idx] = value
IndexError: boolean index did not match indexed array along dimension 0;
dimension is 2661 but corresponding boolean dimension is 5469
The number 5469 correspond to the number of genes in my matrix but I have
no idea what is the 2661 number. I tried different gene sets and the same
error is produced.
Do you have any clue about what might be happening? is the latest version
of anndata likely the problem?
Is there any other information I could share with you to help you to
figure out this issue?
Many thanks,
Ivan
PS. I am really happy with this tool. It has helped me a lot in my project.
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print(anndata.version) Thank you. |
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I'm unable to reproduce an error with my data. Can you please send me your command line and all files used in the command to wot at broadinstitute.org? |
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Sure. I will send it to your broad email as soon as possible. Thanks so much for the quick reply! |
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I fixed the issue which was indeed an issue with anndata. It seems we've found a bug with indexing anndata.core.views.ArrayView. I will try to make a reproducible example of the bug for the anndata team. |
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Thanks! I just ran the code with the corresponding patch and worked fine. I appreciate the quick fix. |
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Hi @joshua-gould , I had the same error but it was fixed when I updated wot installation and I got a new error. |
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Please add compare='all' to diff_exp: |
Hi WOT developers,
I am experiencing some problems with diff_exp after updating wot. I am able to compute the transport maps and the fates matrices but I now get an error regarding data dimensions that I think is related to changes in the anndata object but I just don't know how to fix it.
The error message is:
9 days
BP1 vs BP2, day 6.5, day 6.5
Trying to set attribute
.Xof view, making a copy.Traceback (most recent call last):
File "/homes/iimaz/miniconda3/bin/wot", line 8, in
sys.exit(main())
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/main.py", line 23, in main
cmd.main(args)
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/commands/diff_exp.py", line 71, in main
compare=compare, delta_days=delta_days)
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/tmap/diff_exp.py", line 77, in diff_exp
features=features)
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/wot/tmap/diff_exp.py", line 114, in __do_comparison
scores[np.isnan(scores)] = 0
File "/homes/iimaz/miniconda3/lib/python3.6/site-packages/anndata/core/views.py", line 29, in setitem
container[idx] = value
IndexError: boolean index did not match indexed array along dimension 0; dimension is 2661 but corresponding boolean dimension is 5469
The number 5469 corresponds to the number of genes in my matrix but I have no idea what is the 2661 number. I tried different gene sets and the same error is produced.
Do you have any clue about what might be happening? is the latest version of anndata likely the problem?
Is there any other information I could share with you to help you to figure out this issue?
Many thanks,
Ivan
PS. I am really happy with this tool. It has helped me a lot in my project.
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