Question: openCyto - samples with low cell counts
0
gravatar for Jiang, Mike
3.8 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
 

On 01/21/2016 08:52 AM, Frances Wong wrote:

Good morning, 

 

This is Frances Wong, currently a graduate student at the University of Toronto. I am work on using openCyto to gate my flow Cytometry data but I'm running into some problems. Since I'm doing a screen on 4 separate 96 well plates, I have close to 400 fcs files I would like to gate together but some of the samples have low cell counts and this is causing errors when applying the gating template. Is there an argument to ignore low cell counts? I am currently manually removing these cell counts but I would like a more automated way as I have multiple flowSets I need to analyze. 

 

I was planning on bringing the analysis to the live gate stage and filtering flow low cell counts here but I cannot even apply the singlet gate.  

 

Thank you very much in advanced! 

 

-Frances Wong 


 

 

flowcytometry opencyto • 552 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Jiang, Mike1.2k
Answer: openCyto - samples with low cell counts
1
gravatar for Jiang, Mike
3.8 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

openCyto uses a threshold of event number to determine whether ignore the samples.

getOption("openCyto")

Default is 0, and you can increase it to avoid the pipeline error out,e.g.

options("openCyto" = list(gating = list(minEvents = 300)))
ADD COMMENTlink written 3.8 years ago by Jiang, Mike1.2k

Thank you very very much! It solved the error completely! 

ADD REPLYlink written 3.8 years ago by frances.wong0
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