time_diff

[sizhenran]

Hi Developer,

Thank you for creating this excellent software！

I downloaded it according to the tutorial masscube and prepared the data format, I have two batches that need to be normalized, but I encountered some problems, I tried to add batch in sample_table, but the same error will still appear. The display time is not automatically recognized. How should I solve it?

Welcome to the untargeted metabolomics workflow.

Step 1: Preparing the workflow...
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "F:\software\Scripts\untargeted-metabolomics.exe\__main__.py", line 6, in <module>
    sys.exit(untargeted_metabolomics_workflow())
             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "F:\software\Lib\site-packages\masscube\workflows.py", line 175, in untargeted_metabolomics_workflow
    params._untargeted_metabolomics_workflow_preparation()
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "F:\software\Lib\site-packages\masscube\params.py", line 256, in _untargeted_metabolomics_workflow_preparation
    self.sample_metadata = label_batch_id(self.sample_metadata)
                           ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
  File "F:\software\Lib\site-packages\masscube\utils_functions.py", line 156, in label_batch_id
    t0 = ratio_threshold * np.min(time_diff)
                           ~~~~~~^^^^^^^^^^^
  File "F:\software\Lib\site-packages\numpy\_core\fromnumeric.py", line 3302, in min
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
                          keepdims=keepdims, initial=initial, where=where)
  File "F:\software\Lib\site-packages\numpy\_core\fromnumeric.py", line 86, in _wrapreduction
    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
           ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no identity

<img width="357" height="113" alt="Image" src="https://github.com/user-attachments/assets/36c4029b-8be5-4018-b90e-419dab3dcef5" />

Thanks,



zhenran si

[huaxuyu]

Hi Zhenran,

Thanks for using MassCube.

For batch effect correction, you do not need to input your batch IDs in the sample_table.csv file. MassCube will automatically recognize your batches and apply normalization.

Here is the rule for batch recognition: if the time gap between two raw data files is 10 fold longer than the total analysis time of a single LC-MS experiment, the latter file and files after it will be labeled as the next batch.

To see how the batch IDs are finally determined, go [your_project_folder] -- project_files -- sample_table_with_time.csv

Best,
Huaxu

[sizhenran]

Hi Huaxu，
Thanks for your reply.
Maybe there is something wrong when I converted my files . I just re-prepared the files according to the tutorial and it can run successfully. I will try and explore it again.

Thanks again for your help.

Yours sincerely,
Zhenran