Running diffSplice with paired samples

[albamasmalavila]

Hello,

It's not clear to me how the paired analysis is performed in diffSplice. Do the sample IDs of the two conditions have to match when running diffSplice with -pa parameter? Do they need to be in the same order? In case the sample IDs don't match but -pa parameter is included, will the analysis be run in paired mode by the order of the samples, or it will be run in unpaired mode?

Thank you very much for providing this tool and for your help.

Alba

[EduEyras]

Hi Alba Thanks for your email It will just pair samples in the order they're given. I hope this helps Best E.

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On Thu, 21 May 2026 at 21:29, Alba Mas Malavila ***@***.***> wrote: *albamasmalavila* created an issue (comprna/SUPPA#223) <#223> Hello, It's not clear to me how the paired analysis is performed in diffSplice. Do the sample IDs of the two conditions have to match when running diffSplice with -pa parameter? Do they need to be in the same order? In case the sample IDs don't match but -pa parameter is included, will the analysis be run in paired mode by the order of the samples, or it will be run in unpaired mode? Thank you very much for providing this tool and for your help. Alba — Reply to this email directly, view it on GitHub <#223>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB4JMQHPZKGZ27KEJUL433SBLAVCNFSM6AAAAACZHQXYZSVHI2DSMVQWIX3LMV43ASLTON2WKOZUGQ4TIMJUGQ4DGMI> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[albamasmalavila]

Thank you very much for your fast reply.

I did a test and run the analysis both paired and unpaired and I got exactly the same results. I've been looking at the functions used and I see that the empirical_test function in diff_tools.py doesn't include the paired option as with the classical_test. Even though I don't know how the mathematical calculation is performed, I guess that the empirical test cannot be run in paired mode. Could you confirm that?

Thank you very much,

Alba

[EduEyras]

Yes, sorry, the paired option only works with a classical test. It runs a paired wilcoxon test. Maybe better when you have multiple samples per condition. Best E

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On Fri, 22 May 2026 at 19:00, Alba Mas Malavila ***@***.***> wrote: *albamasmalavila* left a comment (comprna/SUPPA#223) <#223 (comment)> Thank you very much for your fast reply. I did a test and run the analysis both paired and unpaired and I got exactly the same results. I've been looking at the functions used and I see that the empirical_test function in diff_tools.py doesn't include the paired option as with the classical_test. Even though I don't know how the mathematical calculation is performed, I guess that the empirical test cannot be run in paired mode. Could you confirm that? Thank you very much, Alba — Reply to this email directly, view it on GitHub <#223 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB4MNEUUDTLWBLU2LWT44AJMRAVCNFSM6AAAAACZHQXYZSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DKMJXGIZDMOBUGY> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[albamasmalavila]

ok, thank you!

Best,

Alba