How to manually set base landmark in flowStats gaussNorm
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Jiang, Mike ★ 1.3k
Last seen 23 days ago
(Private Address)

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?
Thanks in advance.

Kind regards,

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



flow cytometry flowstats gaussnorm issues • 722 views
Entering edit mode
Jiang, Mike ★ 1.3k
Last seen 23 days ago
(Private Address)


'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'


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

densityplot-after alignment



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