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mmzdouc / FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
https://fermo.bioinformatics.nl/example
MIT License
28 stars 2 forks source link

Cannot upload quantitative biological data (*.csv) file #1

Closed trikaloudis closed 1 year ago

trikaloudis commented 1 year ago

Hello, many thanks for sharing FERMO. I have a problem uploading this .csv file (the other files are ok). The error I get is seen below. Many thanks for your help. Tri

Traceback (most recent call last): File "C:\Users\trika\miniconda3\envs\FERMO\lib\site-packages\pandas\core\indexes\base.py", line 3803, in get_loc return self._engine.get_loc(casted_key) File "pandas_libs\index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas_libs\index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc File "pandas_libs\hashtable_class_helper.pxi", line 2263, in pandas._libs.hashtable.Int64HashTable.get_item File "pandas_libs\hashtable_class_helper.pxi", line 2273, in pandas._libs.hashtable.Int64HashTable.get_item KeyError: 0

The above exception was the direct cause of the following exception:

KeyError: 0

mmzdouc commented 1 year ago

Hi Tri,

thank you for trying out FERMO! May I take a look at the .csv-file that gives you the error when loading it into FERMO? If you do not feel comfortable posting it publicly, you can send it to my university email address: mitja.zdouc(a)wur.nl My guess is that the pandas module (which is used to read the csv files) encounters something unexpected and throws the error, but I would have to see the file to be sure.

Kind regards,

Mitja

mmzdouc commented 1 year ago

Error resolved in FERMO version 0.8.6.

Error was caused by gaps in the index of the Pandas DataFrame, which were introduced by filtering for '0'-values. Fixed by resetting the index of the Pandas DataFrame before further processing.