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Differential Expression between cell population

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gilgifri

Participant

Posts: 2

Joined: Fri Jan 08, 2021 6:43 am

Post Fri Jan 08, 2021 8:17 am

Differential Expression between cell population

Hello,
I am analyzing a CyTOF experiment with two biological conditions, each has 3 replicates. After clustering the cells, there are ~10 cell populations.
Does anyone has recommendations for a tool or for a statistical test for differential expression between cell populations (each cell population includes 2 conditions, and 3 replicates for each condition)?
Thank you
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sgranjeaud

Master

Posts: 125

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Sun Jan 10, 2021 9:40 pm

Re: Differential Expression between cell population

Hi,
IMHO the most rigorous approach is the diffcyt package as featured in the workflow of Nowicka. Look at the Differential analysis paragraph in the middle of the article. I would advice you to read the article carefully in order to understand the whole workflow.
As this experiment ended up with 10 pop, I feel like it does not exploit the discovery power of CyTOF.
As the design consists in only 3 replicates per condition, I feel like this experiment is under powered. How much confidence do you have in an estimation based on 3 measures?
Best,
Samuel
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MCOlivier

Contributor

Posts: 47

Joined: Mon Oct 05, 2015 9:48 am

Location: European Genomic Institute for Diabetes, Universitity of Lille, Institut Pasteur de Lille, France

Post Mon Jan 11, 2021 8:06 am

Re: Differential Expression between cell population

Hi ^^
You could also try MEM, which highlights the differentially expressed markers beetween clusters.
https://github.com/cytolab/mem

Best,
Olivier
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gilgifri

Participant

Posts: 2

Joined: Fri Jan 08, 2021 6:43 am

Post Mon Jan 11, 2021 3:04 pm

Re: Differential Expression between cell population

Thank you for the replies!!
Actually I used the CyTOF workflow of Nowicka et al. (https://pubmed.ncbi.nlm.nih.gov/28663787/). However, it supports only differential expression between conditions, inside a cell population. I am interested also in comparing expression between different cell populations.
I will look also into MEM.
Thank you
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markrobinsonca

Participant

Posts: 11

Joined: Wed Apr 19, 2017 7:35 pm

Post Mon Jan 11, 2021 4:24 pm

Re: Differential Expression between cell population

@gilgifri: Just to say that while the Nowicka workflow doesn't do DE between subpopulations/clusters, it does put the data in a SingleCellExperiment object, which allows you to directly use, for example, the findMarkers() function from the scran package. For example, since you likely have multiple samples, you can add sample as a blocking factor.

More details here:
https://rdrr.io/bioc/scran/man/findMarkers.html

Best, Mark

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