certain samples do not work with flowai

[lopezdavisc]

Hello, I ran cytonorm for batch correction and afterwards, flowai did not seem to work on certain samples. If I run flowai on the original data files, it works on all of them. what could be the reason for this?

[giannimonaco]

Hello, I am not sure why. If you could send me a file I could try to check why. However, as flowAI does only quality control separately for each file, it should be done before normalization. In this way, you avoid normalization of anomalies in the data.

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On Thu, 16 Jun 2022 at 16:14, lopezdavisc ***@***.***> wrote: Hello, I ran cytonorm for batch correction and afterwards, flowai did not seem to work on certain samples. If I run flowai on the original data files, it works on all of them. what could be the reason for this? — Reply to this email directly, view it on GitHub <#11>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC2UTEFHLWQ72BW25QY6EJDVPMZCPANCNFSM5Y66PGDQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[denvercal1234GitHub]

@giannimonaco - Would I please ask whether "normalisation" here also means arcsinh transformation? I follow a spectral flow analysis pipeline that includes a arcsinh step (from the Spectre package) but I want to incorporate flowAI QC. Should I perform flowAI before or after arcsinh transformation?

Thank you.

[giannimonaco]

Hi! Yes, you should run it also before transformation of the data. It is better to perform the QC on non modified data.

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On Thu, Jan 26, 2023 at 9:05 PM Quang Nguyen ***@***.***> wrote: @giannimonaco <https://github.com/giannimonaco> - Would I please ask whether "normalisation" here also means arcsinh transformation? I follow a spectral flow analysis pipeline that includes a arcsinh step (from the Spectre package) but I want to incorporate flowAI QC. Should I perform flowAI before or after arcsinh transformation? Thank you. — Reply to this email directly, view it on GitHub <#11 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC2UTED2XJH66RIZ7D5QZGDWULKH5ANCNFSM5Y66PGDQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>