Re: FlowStats help
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 23 days ago
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Jill,

For this type of two-mode distributions, you can try one of the 2d gating function (flowClust.2d) provided by openCyto package to gate out one population and then use the negate gate for the other.  Here is one reproducible example to get CD3+ and CD3-

library(openCyto)

#load the gated data

dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))

#get the parent data

fs <- getData(gs, "singlets")
fr <- fs[[1]] #get the first sample

# run 2d gating to get CD3+ gate


g <- flowClust.2d(fr, xChannel = "SSC-A", yChannel = "<V450-A>" )

#visualize it
xyplot(`SSC-A`~`CD3`, fr,  xbin = 32, smooth = F, stats = T, filter = g)

 

Mike

On 03/11/2015 08:44 AM, Jill M Trivedi wrote:

Hello,

I have this flow cytometry data that I am attempting to analyze with flowStats. However, I am finding it difficult to find a gating function that recognizes the two populations based on density. Is there any particular gate you would recommend to do this? or a combination of gates?

 

Thanks,

Jill Trivedi

 

flowclust opencyto flowcytometry • 859 views
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