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2020-Trussart et al-preprint

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mleipold

Guru

Posts: 2156

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed May 13, 2020 5:00 pm

2020-Trussart et al-preprint

"CytofRUV: Removing unwanted variation to integrate multiple CyTOF datasets"
Marie Trussart, Charis E Teh, Tania Tan, Lawrence Leong, Daniel HD Gray, Terence P. Speed
bioRxiv, posted May 09, 2020
https://doi.org/10.1101/2020.05.09.085621

- will update when/if this is peer-reviewed and published

- compares to CytoNorm and BatchAdjust

- "The fcs files from this study will be available at flow repository ID FR-FCM-Z2L2." "Sorry, you do not have access to the specified experiment."

- also reuses datasets
1. 2019-Schuyler et al-Front Immunol
2. FR‐FCM‐Z247 (2019-Van Gassen et al-Cytometry A)
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narulam

Participant

Posts: 5

Joined: Sun Mar 29, 2020 10:28 am

Post Wed May 27, 2020 8:09 pm

Re: 2020-Trussart et al-preprint

I tried this normalizing algorithm for raw fcs files. It works well for batch effect correction but markers lose resolution between negative and positive expression due to normalized protein distribution which makes it very difficult to manually gate subpopulations (for eg. Tregs and CD4+ Th subsets) and identify separated islands with tsne or downstream clustering differences. Any thoughts on that?

Thanks
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dtelad11

Master

Posts: 112

Joined: Mon Oct 31, 2016 6:26 pm

Post Wed May 27, 2020 8:14 pm

Re: 2020-Trussart et al-preprint

Any chance you could post before/after biaxial plots?
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narulam

Participant

Posts: 5

Joined: Sun Mar 29, 2020 10:28 am

Post Sun May 31, 2020 11:46 pm

Re: 2020-Trussart et al-preprint

Hi El-ad,

I've attached some slides to show the gating and resolution issue for some markers. Since the scaling from pre-CytofRUV files does not apply to the files post normalization, I tried to tweak the scaling on normalized fcs files and was able to improve the resolution for some of them (Th1,Th2,Th17) but not all (Treg,Tfh). Please let me know your thoughts.

Thanks,
Mansi
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mleipold

Guru

Posts: 2156

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Jun 01, 2020 12:05 am

Re: 2020-Trussart et al-preprint

Hi Mansi,

Your files didn't attach.

There could be a couple reasons for this:
1. You might not have hit "Add the file" after you chose it for upload.
2. The file size might have been too big to attach. I'm not sure of the max file size allowable, but this has happened before (eg viewtopic.php?f=4&t=1496&p=4240)


Mike
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narulam

Participant

Posts: 5

Joined: Sun Mar 29, 2020 10:28 am

Post Tue Jun 02, 2020 8:30 pm

Re: 2020-Trussart et al-preprint

Hi,

I split up the files due to size limit and attached now. Please let me know your thoughts.

Thanks,
Mansi
Attachments
CytofRUV_2.pptx.zip
(799.94 KiB) Downloaded 17 times
gatingTfh.png
Gating.Tregs.png

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