How to import an integrated data from seurat V3 to dyno?

[Dongxu-Zheng]

Hi, thanks for developing such a great package for trajectory analysis. Maybe this is a problem not a issue. If I post it in a wrong place, just let me know and show me a right direction.

I have 4 samples and they do have some batch effect. So I use scTransform workflow to integrate them together using seurat V3. My question is how to import a integrated data to dyno? If I still use the original read count matrix, the batch effect will also be introduced into dyno. Or is there any way to remove the batch effect in dyno?

Thanks for any suggestions and advices in advance!

Issac

[wfma]

also want to know this^

[rcannood]

Hello @Dongxu-Zheng !

Can you send me an example data object you wish to run with dyno?

Kind regards, Robrecht

[Dongxu-Zheng]

Hello @Dongxu-Zheng !

Can you send me an example data object you wish to run with dyno?

Kind regards, Robrecht

Hi Robrecht,

Thanks for your reply. I am not allowed to send the whole dataset to you due to confidentiality. But I can send you a subset of the integrated object created by Seurat V3. By the way, where to find your email or how to share it with you?

Thanks! Dongxu

[rcannood]

No need to send me the whole dataset, a tiny part of it is okay.

You can send it to '[email protected]'.

[VeredasCA]

Hi! I'm interested in this question. Was it solved? If so, could you share the solution? Thank you!

Veredas

[Dongxu-Zheng]

Hi, unfortunately, I didn’t get any reply. To remove the batch effect, my suggestion is to use a UMAP embedding matrix for trajectory analysis.

From: VeredasCA @.> Sent: vrijdag 27 augustus 2021 11:49 To: dynverse/dyno @.> Cc: Zheng, D. (HG) @.>; Mention @.> Subject: Re: [dynverse/dyno] How to import an integrated data from seurat V3 to dyno? (#95)

Hi! I'm interested in this question. Was it solved? If so, could you share the solution? Thank you!

Veredas

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[VeredasCA]

Oh, I see.. Thank you @Dongxu-Zheng for your quick answer and for your suggestion!