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Internal Error in computing differential expression

See original GitHub issue

I have an internal server error while computing differential expression. When I select two groups of cells and click compute, it shows this error:

And in the terminal, this message appears:

[2019-05-07 09:25:01,167] ERROR in app: Exception on /api/v0.2/data/var [PUT]
Traceback (most recent call last):
TypeError: 'coo_matrix' object is not subscriptable

I didn’t have this problem before, started to see with v0.9.1, tried with the same files I’m working with and having same error. This is one of the datasets that I’m working with: https://drive.google.com/open?id=14LCnlBRwz_gZRvd0p9NzNp_kuHylbcms

Issue Analytics

State:
Created 4 years ago
Comments:7 (5 by maintainers)

Top GitHub Comments

1reaction

bkmartinjrcommented, May 9, 2019

@cakirb - very happy to help. The only caveat I’ll add is that I am currently trying to better characterize our advice, and will update the FAQ as more info is available. If you find any interesting performance observations, please let me know (either on github, or feel free to join our slack channel).

1reaction

bkmartinjrcommented, May 7, 2019

Thank you @cakirb – really appreciate the test data set.

While I am debugging this, you may be able to work around the bug by using a CSC (columnar) sparse format for the expression data (X), instead of a CSR format. cellxgene is generally faster if you use formats that allow fast columnar access, as most of the data access is along that axis.