Open npaisaca opened 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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Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
— Reply to this email directly, view it on GitHubhttps://ddec1-0-en-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fgithub.com%2fkuanrongchan%2fSTAGES%2fissues%2f18%23issuecomment%2d1948127172&umid=ebf0c089-9691-4be6-9981-3ac9d691682b&auth=3eee6d57317a38631073652579c10dc620ca2b41-d8bd04b50800a7a13225cf958d84bde06a11e208, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVYMKCJAYLFT6JNTYLCTYKTYT4YQNAVCNFSM6AAAAABDLXSJUOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBYGEZDOMJXGI. You are receiving this because you commented.Message ID: @.***>
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Hi,
I tried to use the demo dataset as you suggested and it worked fine. I spoke to my supervisor, who asked me to send only part of the data, I hope that's okay for you. Otherwise, the format of the files is exactly the same as the ones I've been uploading.
Thank you for your help!
El vie, 16 feb 2024 a las 11:42, Kuan Rong Chan @.***>) escribió:
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
— Reply to this email directly, view it on GitHub< https://ddec1-0-en-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fgithub.com%2fkuanrongchan%2fSTAGES%2fissues%2f18%23issuecomment%2d1948127172&umid=ebf0c089-9691-4be6-9981-3ac9d691682b&auth=3eee6d57317a38631073652579c10dc620ca2b41-d8bd04b50800a7a13225cf958d84bde06a11e208>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AVYMKCJAYLFT6JNTYLCTYKTYT4YQNAVCNFSM6AAAAABDLXSJUOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBYGEZDOMJXGI>.
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Hi:
Sure thing! You can try on the truncated dataset yourself and see if you see a similar problem. If it does, please let us know. We will see how we can help!
Best regartds Kuan Rong
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.comhttp://kuanrongchan.com
From: npaisaca @.> Sent: Monday, February 19, 2024 4:42 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi,
I tried to use the demo dataset as you suggested and it worked fine. I spoke to my supervisor, who asked me to send only part of the data, I hope that's okay for you. Otherwise, the format of the files is exactly the same as the ones I've been uploading.
Thank you for your help!
El vie, 16 feb 2024 a las 11:42, Kuan Rong Chan @.***>) escribió:
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
— Reply to this email directly, view it on GitHub< https://ddec1-0-en-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fgithub.com%2fkuanrongchan%2fSTAGES%2fissues%2f18%23issuecomment%2d1948127172&umid=ebf0c089-9691-4be6-9981-3ac9d691682b&auth=3eee6d57317a38631073652579c10dc620ca2b41-d8bd04b50800a7a13225cf958d84bde06a11e208>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AVYMKCJAYLFT6JNTYLCTYKTYT4YQNAVCNFSM6AAAAABDLXSJUOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBYGEZDOMJXGI>.
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Hello,
I just tried processing the truncated dataset and I get the same error on the same step.
Thanks!
El lun, 19 feb 2024 a las 9:45, Kuan Rong Chan @.***>) escribió:
Hi:
Sure thing! You can try on the truncated dataset yourself and see if you see a similar problem. If it does, please let us know. We will see how we can help!
Best regartds Kuan Rong
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.comhttp://kuanrongchan.com
From: npaisaca @.> Sent: Monday, February 19, 2024 4:42 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi,
I tried to use the demo dataset as you suggested and it worked fine. I spoke to my supervisor, who asked me to send only part of the data, I hope that's okay for you. Otherwise, the format of the files is exactly the same as the ones I've been uploading.
Thank you for your help!
El vie, 16 feb 2024 a las 11:42, Kuan Rong Chan @.***>) escribió:
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
— Reply to this email directly, view it on GitHub<
or unsubscribe<
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Sure thing. Please send us the dataframe that you have used for the analysis so we can help troubleshoot. Thanks!
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.comhttp://kuanrongchan.com
From: npaisaca @.> Sent: Monday, February 19, 2024 4:51 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hello,
I just tried processing the truncated dataset and I get the same error on the same step.
Thanks!
El lun, 19 feb 2024 a las 9:45, Kuan Rong Chan @.***>) escribió:
Hi:
Sure thing! You can try on the truncated dataset yourself and see if you see a similar problem. If it does, please let us know. We will see how we can help!
Best regartds Kuan Rong
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.com<https://ddec1-0-en-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fkuanrongchan.com%26gt&umid=ea49f745-b89a-402b-a112-2d1316fe966b&auth=3eee6d57317a38631073652579c10dc620ca2b41-6e5420be9cb62f42dc5a7ed6ef5cba4c4ad85727;
From: npaisaca @.> Sent: Monday, February 19, 2024 4:42 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi,
I tried to use the demo dataset as you suggested and it worked fine. I spoke to my supervisor, who asked me to send only part of the data, I hope that's okay for you. Otherwise, the format of the files is exactly the same as the ones I've been uploading.
Thank you for your help!
El vie, 16 feb 2024 a las 11:42, Kuan Rong Chan @.***>) escribió:
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
— Reply to this email directly, view it on GitHub<
or unsubscribe<
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I'm attaching the files. Thank you!
El lun, 19 feb 2024 a las 9:53, Kuan Rong Chan @.***>) escribió:
Sure thing. Please send us the dataframe that you have used for the analysis so we can help troubleshoot. Thanks!
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.comhttp://kuanrongchan.com
From: npaisaca @.> Sent: Monday, February 19, 2024 4:51 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hello,
I just tried processing the truncated dataset and I get the same error on the same step.
Thanks!
El lun, 19 feb 2024 a las 9:45, Kuan Rong Chan @.***>) escribió:
Hi:
Sure thing! You can try on the truncated dataset yourself and see if you see a similar problem. If it does, please let us know. We will see how we can help!
Best regartds Kuan Rong
Chan Kuan Rong, PhD | Senior Principal Research Scientist, Emerging Infectious Diseases | Duke-NUS Medical School | Tel: 65 90058277 | 8 College Road, Singapore 169857 | kuanrongchan.com< https://ddec1-0-en-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fkuanrongchan.com%26gt&umid=ea49f745-b89a-402b-a112-2d1316fe966b&auth=3eee6d57317a38631073652579c10dc620ca2b41-6e5420be9cb62f42dc5a7ed6ef5cba4c4ad85727;
From: npaisaca @.> Sent: Monday, February 19, 2024 4:42 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
- External Email -
Hi,
I tried to use the demo dataset as you suggested and it worked fine. I spoke to my supervisor, who asked me to send only part of the data, I hope that's okay for you. Otherwise, the format of the files is exactly the same as the ones I've been uploading.
Thank you for your help!
El vie, 16 feb 2024 a las 11:42, Kuan Rong Chan @.***>) escribió:
Hi!
Sure thing. You can try the demo dataset that is already pre-loaded into STAGEs to better understand how the webtool works. Feel free to reach out if you face any issues
Best regards 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 6:31 PM To: kuanrongchan/STAGES @.> Cc: Chan Kuan Rong @.>; Comment @.> Subject: Re: [kuanrongchan/STAGES] Overflow Error in Differential Expression Analysis (Issue #18)
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Hi, the data I'm using is not mine, so I'll have to check first if it's okay for me to send it. In the meantime, is there something I could do or try? Thanks for the quick response!
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Hi,
Thank you for spotting a bug!
I've added a fix that may help. Briefly, the error occurred because there were some -log10 p-values that were too large (infinity) and could not be rounded off when trying to create a y-axis limit in the volcano plot. I've replaced these values with a maximum value of 100 only for the volcano plot.
You may try the web app again with your original dataset.
Do let us know if the error persists or any other errors occur.
Cheers, Clara
Hello,
the fix seems to work for the truncated dataset I sent earlier, but I still get the same error for my full data files. Is it possible that the number of genes of my input is too high and that's what's giving an error?
Also, when processing the truncated files, the log2 fold change that the app returns for the DEGs is different than the original ratio values from the files that I'm uploading, but the p-value is the same. Is this normal?
Thanks for everything!
El lun, 19 feb 2024 a las 10:50, kohcl17 @.***>) escribió:
Hi,
Thank you for spotting a bug!
I've added a fix that may help. Briefly, the error occurred because there were some -log10 p-values that were too large (infinity) and could not be rounded off when trying to create a y-axis limit in the volcano plot. I've replaced these values with a maximum value of 100 only for the volcano plot.
You may try the web app again with your original dataset.
Do let us know if the error persists or any other errors occur.
Cheers, Clara
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Hi,
I've tested for p-values that may occur but am unable to reproduce the error. May I know how large (number of rows) your original dataset is?
As for log2FC values, they're just log2-transformed ratio values.
Regards, Clara
Hello,
the original dataset are three csv files, one of 1,8MB (25313 rows), one of 1,9MB (25135 rows), and one of 2,0MB (24825 rows). I usually upload the three of them at the same time, but the error also appears if I go one at a time.
Thanks and sorry for the inconvenience!
El mar, 20 feb 2024 a las 7:47, kohcl17 @.***>) escribió:
Hi,
I've tested for p-values that may occur but am unable to reproduce the error. May I know how large (number of rows) your original dataset is?
As for log2FC values, they're just log2-transformed ratio values.
Regards, Clara
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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!