ValueError: cannot reindex from a duplicate axis

[teichlab]

ValueError: cannot reindex from a duplicate axis

[mvento]

@HichamAffia Thanks, we try to check it ASAP.

Thanks for your patience

[saeedfc]

HI @mvento ,

It was again an issue of R giving an extra column for serial numbers as rownames. I removed it and then ran it. Went fine.

[ai4pharma]

Same problem here, I also tried to remove duplicate gene symbols in my table and still got the same problem. My cell type are all characters, while there are "-" and numerical values in my cell id.

Here is the header lines or my error messages.
return callback(*args, **kwargs)
File "/miniconda2/envs/cellphonedb/lib/python3.6/site-packages/cellphonedb/src/api_endpoints/terminal_api/method_terminal_api_endpoints/method_terminal_commands.py", line 82, in analysis
deconvoluted_result_name,

[mvento]

Hi @HichamAffia,

corresponding to the clusters numbers, could it be the issue can be an issue. We will try to replicate your issue. Can you send us your inputs? (or part of that)

Thanks

[HichamAffia]

Hi @mvento ,

Here is a subset that gives me the same error.
input_subset_issue_3.zip

Thanks

[hejian41]

Also encountered the same problem, is there any solutions? @HichamAffia

Here are error messages.
.......
File "/home/hejian/cpdb-venv/lib/python3.6/site-packages/pandas/core/internals.py", line 4414, in reindex_indexer
self.axes[axis]._can_reindex(indexer)
File "/home/hejian/cpdb-venv/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 3576, in _can_reindex
raise ValueError("cannot reindex from a duplicate axis")
ValueError: cannot reindex from a duplicate axis

thanks

[mvento]

Hi @HichamAffia,

This is because all data is filtered (we only support human genes yet).

We fix this crash in the next release.

Cheers

[mvento]

Hi @hejian41 and @Huang-Ying ,

can you send your input data (or a part of that) to [email protected] for debug purposes?

Thanks

[hejian41]

I checked my data and find there were some duplicated rownames. No error reported after the those genes removed! @mvento

Thanks !

[mvento]

hi @hejian41,

Perfect! we are working on better error reporting.

Cheers

[HichamAffia]

Hi @mvento , thanks!
I converted mouse Ensembl IDs to Human, and checked for duplicate gene IDs. Seems to work fine with no change to the cluster names (still numeric)!

[saeedfc]

Same error here for me! All my Genes are human ensemble IDs and are unique. Any solutions yet?

[mvento]

Hi @saeedfc,

We are working on a better error report. Can you send us your data (or a part of that) to us?

Thanks!

[mvento]

Hi all,

We have released the version v.1.1.0 of CellPhoneDB. These errors are checked now to prevent app crash.

We have added error messages and we are working on a better documentation of the errors to help to the user.

Thanks for using CellPhoneDB!