kuanrongchan
commented
8 months ago Hi!
Mind sharing your uploaded dataset and let us see how we can help troubleshoot?
Best Kuan Rong
Chan Kuan Rong | Senior Principal Research Scientist | Duke-NUS Medical School | Programme in Emerging Infectious Diseases, Singapore | Tel: +65 90058277<tel:+65%2090058277> | 8 College Road, Singapore 169857 | Website: kuanrongchan.com
From: npaisaca @.> Sent: Friday, February 16, 2024 5:51 PM To: kuanrongchan/STAGES @.> Cc: Subscribed @.***> Subject: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -Hello, I have recently started using STAGES with RNA-seq data. I did the statistical analysis previously with Rstudio and generated three csv files with p-values and ratios of three different comparisons. When I upload these files to STAGES, the app initially returns no error and lets me proceed up until the Differential Expression Analysis step, where I get this error:
OverflowError: cannot convert float infinity to integer Traceback: File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 535, in _run_script exec(code, module.dict) File "/app/pages/04_Differential_Expression_Analysis.py", line 116, in vol_plot, iplot = preDE.volcano( File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 212, in wrapper return cached_func(*args, *kwargs) File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 241, in call return self._get_or_create_cached_value(args, kwargs) File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 268, in _get_or_create_cached_value return self._handle_cache_miss(cache, value_key, func_args, func_kwargs) File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 324, in _handle_cache_miss computed_value = self._info.func(func_args, **func_kwargs) File "/app/helper_functions/degs.py", line 186, in volcano max_y = math.ceil(mini_df[pval_name].max()) if math.ceil(mini_df[pval_name].max()) > max_y else max_y
I tried to upload only one file at a time from both the online webtool and locally, but I keep getting the same error. I also tried uploading the files in different format (txt and xlsx), but the app returns the datasets as empty and won't even let me proceed to Pre-processing. What should I do?
Thanks in advance!
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npaisaca
kohcl17
Hello, I have recently started using STAGES with RNA-seq data. I did the statistical analysis previously with Rstudio and generated three csv files with p-values and ratios of three different comparisons. When I upload these files to STAGES, the app initially returns no error and lets me proceed up until the Differential Expression Analysis step, where I get this error:
OverflowError: cannot convert float infinity to integer Traceback: File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 535, in _run_script exec(code, module.dict) File "/app/pages/04_Differential_Expression_Analysis.py", line 116, in
vol_plot, iplot = preDE.volcano(
File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 212, in wrapper
return cached_func(*args, *kwargs)
File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 241, in call
return self._get_or_create_cached_value(args, kwargs)
File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 268, in _get_or_create_cached_value
return self._handle_cache_miss(cache, value_key, func_args, func_kwargs)
File "/usr/local/lib/python3.10/site-packages/streamlit/runtime/caching/cache_utils.py", line 324, in _handle_cache_miss
computed_value = self._info.func(func_args, **func_kwargs)
File "/app/helper_functions/degs.py", line 186, in volcano
max_y = math.ceil(mini_df[pval_name].max()) if math.ceil(mini_df[pval_name].max()) > max_y else max_y
I tried to upload only one file at a time from both the online webtool and locally, but I keep getting the same error. I also tried uploading the files in different format (txt and xlsx), but the app returns the datasets as empty and won't even let me proceed to Pre-processing. What should I do?
Thanks in advance!