Investigate negative peak in CyTOF

The peak at far left is observed in CyTOF data often time (even after transformation).

inverseTrans <- getTransformations(gh, inverse = T)[[1]] 
chnl <- '(Gd158)Dd'
marker <- "CD45RA"
data <- getData(gh)
raw <- transform(data, transformList(chnl, inverseTrans))
fs <- as(list(raw = raw, trans = data), "flowSet")
f1 <- as.formula(paste0("~", marker))
densityplot(f1, fs, channels = chnl, main = paste("tranformed", marker), margin = F, stack = F)

Based on the downstream “CD45RA, CCR7” gate, it is apparently not the negative population that gate should be referenced to. (the gate cut at around 5k, but this negative peak sits below 2.5k)

plotGate(gh, "CD4/Q1: CD45RA- , CCR7+", checkName = F, raw.scale = F)

So we are trying to find out what exactly this negative peak is by using overlay plots.

First, gate out that population (named as unkown peak) and add it to gating tree.

g <- mindensity(data, "(Gd158)Dd", positive = F)
add(gh, g, parent = "root", name = "unkown peak")

## [1] 118

recompute(gh, "unkown peak")
plotGate(gh, "unkown peak", checkName = F, type = "densityplot")

plotGate(gh, "unkown peak", checkName = F, default.y = "Cell_length")

Then display this poulation on its relavant gates

nodePath <- getNodes(gh)[grepl("CD4/Q1: CD45RA- , CCR7\\+", getNodes(gh))]
pops <- nodePath
while(nodePath!="/"){
  nodePath <- dirname(nodePath)
  pops <- c(nodePath, pops)
  }
plotGate(gh, pops[-1], checkName = F)

plotGate(gh, pops[-1], checkName = F, overlay = "unkown peak")