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Recommendation on an example data

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jonsnow

Participant

Posts: 2

Joined: Mon Nov 02, 2020 2:15 pm

Post Tue Nov 03, 2020 4:36 pm

Recommendation on an example data

Hi,I'm new to CyTOF data. I'm wondering whether someone can recommend me an example dataset that I can test the preprocessing step (normalization, debarcoding, compensation) and downstream analysis. Thanks in advance.
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Nov 03, 2020 7:24 pm

Re: Recommendation on an example data

Hi Jon,

Unfortunately, off the top of my head, I'm not sure there's a single dataset that has had every kind of data transformation applied to it.

1. Normalization. Very common. Still a divide between the Fluidigm method and the Finck et al method. Here's a dataset where we ran the Raw files through each of the normalizers: http://flowrepository.org/id/FR-FCM-ZYAJ
2. Debarcoding. Very common; you should be able to use any dataset that uses BC reagents (Fluidigm or in-house; small molecule or antibody-driven).

3. Compensation to remove spillover (comp'ing, similar to regular flow). Very rare at the moment. Main examples are Chevrier et al (https://doi.org/10.1016/j.cels.2018.02.010 ; https://data.mendeley.com/datasets/v58yj49pfr/1 ) and Budzinski et al (https://doi.org/10.4049/jimmunol.1801640 ; dataset not publicly available to my knowledge ; uses Chevrier algorithm)
4. Batch correction. Relatively uncommon, partly because there's still a lot of work in the area trying to understand best way(s) to do this for CyTOF data. Examples include but are not limited to CytofRUV, CytoNorm and BatchAdjust


Mike
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jonsnow

Participant

Posts: 2

Joined: Mon Nov 02, 2020 2:15 pm

Post Tue Nov 03, 2020 10:03 pm

Re: Recommendation on an example data

Thank you Mike. I'll take a look at the links you shared. -Jon

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