Error using GatingSet

[EVatareck]

Hello,

I have an issue using GatingSet with data obtained from a MACSQuant. I used the command several times before with data from other devices, but it seems that it does not work with the MACSQuant data. I get the following error:

Error in (function (cond) :
error in evaluating the argument 'x' in selecting a method for function 'GatingSet': Not compatible with requested type: [type=character; target=double].

This is my minimal example code:
################################
library(flowCore)

rawdata <- read.flowSet(path = "./Flowcore_Test/", emptyValue = F)

pData(rawdata)$sample <- "test"

trTransform <- transformList(colnames(rawdata),
truncateTransform(transformationId = "tr", a = 1),
transformationId = "tr")

lTransform <- transformList(colnames(rawdata),
logTransform(transformationId = "log10", logbase=10, r=1, d=1),
transformationId = "log10")

trData <- transform(rawdata, trTransform)
lData <- transform(trData, lTransform)
summary(lData)

Gating

rGate <- rectangleGate(filterId="GFP", "FL3-A"=c(0.5, 3))
gsData <- GatingSet(lData)

cannot proceed with the following

gs_get_pop_paths(gsData)
gs_pop_add(gsData, rGate, parent = "root")
###########################################

Here, I uploaded the small example dataset:
https://drive.google.com/drive/folders/164sMG67N6RPXwi16pnWM_VWTlYu8NCSN

What am I doing wrong?
I'd highly appreciate any help, as I would really need to gate my dataset. :(

Thank you very much in advance!
Elisabeth

[EVatareck]

Hello,
could anybody help? Or do you need any further information in order to adress the issue?
Thank you so much!

[DillonHammill]

I would seriously consider using CytoExploreR for this type of analysis. CytoExploreR will take care of all these steps for you, and you can interactively draw gates!
https://dillonhammill.github.io/CytoExploreR/

[rpahl]

In case this is still of relevance to someone. I had a similar issue with data coming from MACSQuant, which in my case was caused by an empty keyword entry set by MACSQuant, specifically "$SPILLOVER" was given a matrix <0 x 0>. So if you have something like this, check your keywords after you have read your file (you also may have to read in via flowCore::read.FCS(filename, emptyValue = FALSE).

If you have a similar issue, fwiw I just wrote a function to cleanup empty keyword entries

sanitize_keywords <- function(fr)
{
    stopifnot(fr |> methods::is("flowFrame"))

    emptyKeywords <- Filter(flowCore::keyword(fr), f = \(x) length(x) == 0)
    for (key in names(emptyKeywords)) {
        flowCore::keyword(fr)[[key]] <- NULL
    }
    fr
}