Counts between analyze_sample and FlowJo output are different
mgratigny opened this issue · 5 comments
Describe the bug
Hi,
I’m trying to a FlowJo workspace to extract counts and relative abundances (fréquemment of parents) as it can be done with FlowJo.
I load a given workspace with associated FCS sample and I execute the tutorial to analyze results as describe in flowkit-tutorial-part06-workspace-class.ipynb on my data.
When I do that, if I compare the count column and results obtains by the biologist, the results are slightly different. Sometime I have the exact value and sometime it is different.
When I look for the content directly inside the .wsp file I show some « count » item inside the « Population » elements.
And example here:
<Population name="Leukocytes" annotation="" owningGroup="All Samples" expanded="1" sortPriority="10" count="90001" >
The Count observe in the XML is the same that FlowJo can export.
Is there a way to collect these counts and associated « frequency of parents » from these Count items ?
Do you know why I observe some differences when I use the « analyze_sample » method ?
Than you very much for your help
Best regards
Code To Reproduce
Code to reproduce the behavior:
import os
import flowkit as fk
sample_path = "./path_to_dir"
wsp_path = os.path.join(sample_path, "file.wsp")
wsp = fk.Workspace(wsp_path, fcs_samples=sample_path)
sample_group='All Samples'
sample_id = "one_sample_selected"
wsp.analyze_samples(sample_group, verbose=True)
results_report = wsp.get_analysis_report(sample_group)
sample_results = wsp.get_gating_results(sample_id)
sample_results.report...
Expected behavior
Is there a way to collect these counts and associated « frequency of parents » from these Count items ?
Desktop (please complete the following information):
- OS: Mac OS ventura 13.5.1
- Python 3.11.4
- FlowIO 1.1.1
- FlowKit 1.0.1
- FlowUtils 1.0.0
Hi,
Yes there are differences in some gates between FlowJo & FlowKit as FlowJo processes gates on binned event data. I wrote a more detailed response explaining this here:
Hope that helps to explain what is happening,
Scott
Thank you very much for your answer.
Is there a way to extract FlowJo count value from "count" easily using flowkit ?
No, afraid not. The best way to get that data would be from an export of the statistics from FlowJo.
Thank you for your answer and for Flowkit ! It is a great tool !
Thanks for using it and please submit any issues you may find in the future.