How to manually set base landmark in flowStats gaussNorm
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 23 days ago

Hi Mike,

I have a question regarding to the gaussNorm method of the package flowStats. I want to specify the base landmarks used for the normalization on my own. How can I do this? The argument base.lms says: A list of vector for each channel that contains the base landmarks for normalizing that channel. If not specified the base landmarks are computed from the set of extracted landmarks.
But I can not find any example how to use this. If I use it I think max.lms should be NULL and both thresholds as well, right? Can you give me one example how to use this parameter?

Kind regards,
Joachim

--
M. Sc. Joachim Schumann
PhD Student
Department of Environmental Microbiology
AG Flow Cytometry
Helmholtz Centre for Environmental Research - UFZ
Permoserstraße 15, 04318 Leipzig
Tel.: 0049-341-235-1330
E-Mail: joachim.schumann@ufz.de
http://www.ufz.de 

flow cytometry flowstats gaussnorm issues • 722 views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 23 days ago

Joachim,

'base.lms' was not well documented. After stepping into the source code, I found out that it is the mode/peak positions. When you want to manually set the base landmarks, simply plot the densityplot  of the target sample on the target channel and find the x coordinates of the peak apex that you want to use as the base landmarks. Here is the illustration based on the examples in '?gaussNorm'

library(flowStats)
library(ggcyto)

data(ITN)
dat <- transform(ITN[1:3], "CD4"=asinh(CD4), "CD3"=asinh(CD3), "CD8"=asinh(CD8))
lg <- lymphGate(dat, channels=c("CD3", "SSC"),preselection="CD4",scale=1.5)
dat <- Subset(dat, lg$n2gate) #inspect densityplot to estimate landmarks by hand ggcyto(dat[[1]], aes(x = "CD8", col = name)) + geom_density() #manaully supply the base landmarks in gaussNorm datr <- gaussNorm(dat, "CD8", base.lms = list(CD8 = c(1.58, 6.68)))$flowset
#before normailzation
ggcyto(dat, aes(x = "CD8", col = name)) + geom_density() + facet_null()

#after the normalization
ggcyto(datr, aes(x = "CD8", col = name)) + geom_density() + facet_null()