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giannimonaco / flowAI

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certain samples do not work with flowai #11

Open lopezdavisc opened 2 years ago

lopezdavisc commented 2 years ago

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 commented 2 years ago

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.

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 https://github.com/giannimonaco/flowAI/issues/11, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2UTEFHLWQ72BW25QY6EJDVPMZCPANCNFSM5Y66PGDQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

denvercal1234GitHub commented 1 year ago

@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 commented 1 year ago

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

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 https://github.com/giannimonaco/flowAI/issues/11#issuecomment-1405583968, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2UTED2XJH66RIZ7D5QZGDWULKH5ANCNFSM5Y66PGDQ . You are receiving this because you were mentioned.Message ID: @.***>