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Error while writing annData #1143
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It looks like the problematic column ( I would suggest trying something like: |
@ivirshup Is there a better way of doing this? Additionally just saving everything as a category isn't always useful, since some "object" type columns are actually int/float columns. So I need to go through each column and check whether they are better saved as categories or floats/int before saving. |
@ivirshup Thank you very much it worked! |
Please make sure these conditions are met
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Hi Everyone,
First of all, thank you very much for this wonderful tool.
I'm reopening an issue, which seems to have affected other users. Such as https://github.com/scverse/anndata/issues/726.
I created an Anndata object based on RNA and HTO data for hashing demultiplexing. No problem there, however when I try to to add the results from demultiplexing I run in the already seen:
I opened a csv file as a dataframe, which contains the results from demultiplexing with BFF. The results look like this:
Barcode | BFF
TTTGTCATCTTACCTA-1 | negative
TTTGTCATCTTAGAGC-1 | negative
TTTGTCATCTTAGCCC-1 | HTO_BBX-1
TTTGTCATCTTATCTG-1 | negative
TTTGTCATCTTCAACT-1 | negative
TTTGTCATCTTCATGT-1 | negative
TTTGTCATCTTCCTTC-1 | negativ
Which is pretty standard for demultiplexing results.
The code throwing this error is:
Code:
The error looks like this:
I would appreciate any assistance you could provide.
Thank you very much in advance!
Versions
anndata 0.9.2
mudata 0.2.3
numpy 1.24.4
pandas 2.0.3
scanpy 1.9.3
session_info 1.0.0
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