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Question: OpenCyto - getting gate coordinates
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gravatar for Ulrik Stervbo
2.1 years ago by
Germany
Ulrik Stervbo30 wrote:

I would like to be able to identify samples where the gating applied with opencyto is odd. Instead of inspecting each sample, I am thinking of plotting the gate coordinates. Is this possible?

Thanks in advance.

Ulrik

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Ulrik Stervbo30
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gravatar for Jiang, Mike
2.1 years ago by
Jiang, Mike1.1k
(Private Address)
Jiang, Mike1.1k wrote:

The cell population statistics (e.g. proportions or counts) can be used to perform the outlier detection. You can check out QUALIFIER package.  But if you decide the package is a little over complicated for you, you can also do it own your own. i.e. extract proportions by `getPopstats` for each population and call outliers using your own criteria or function or visualize it with `ggplot`.

 

ADD COMMENTlink written 2.1 years ago by Jiang, Mike1.1k

True that strange proportions are indication of strange gates (I am also using at the CV as you do in https://www.bioconductor.org/help/course-materials/2015/BioC2015/OpenCytoWorkshop.html) but I also need to adjust strange gates that might not give rise to strong outliers. We still inspect the samples visually and oddly placed gagtes (no matter the effect) will raise questions.

ADD REPLYlink written 2.1 years ago by Ulrik Stervbo30
0
gravatar for Ulrik Stervbo
2.1 years ago by
Germany
Ulrik Stervbo30 wrote:

I just came across getGate(). Extraction of values depend on the gate but could be the way forward

ADD COMMENTlink written 2.1 years ago by Ulrik Stervbo30
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