Question: Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
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gravatar for Lucy
4 weeks ago by
Lucy40
Lucy40 wrote:

Hi,

I would like to use Harmony to remove batch effects from my 10x Genomics scRNA-seq data combined from three donors. However, I am wondering whether Harmony requires the same cell populations to be present in all samples, or how it deals with a population that is e.g. unique to one donor?

Many thanks,

Lucy

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Lucy40

looks like it requires same population.

ADD REPLYlink written 4 weeks ago by shoujun.gu250
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gravatar for igor
4 weeks ago by
igor8.8k
United States
igor8.8k wrote:

No. They illustrate that a point with the main figure on their tutorial page:

enter image description here

Harmony uses fuzzy clustering to assign each cell to multiple clusters, while a penalty term ensures that the diversity of datasets within each cluster is maximized.

ADD COMMENTlink written 4 weeks ago by igor8.8k
0
gravatar for Lucy
4 weeks ago by
Lucy40
Lucy40 wrote:

Thanks, this shows cell types that are present in two out of the three datasets. Does this work equally well if one of your populations is only present in a single dataset?

ADD COMMENTlink written 4 weeks ago by Lucy40
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