I have a question about how the LymphGate function works in R.  Can you tell me what transformation is being performed on the dataset.  I assumed that you could set parameters so that there would be no transformation applied, but when I run the following script, my dataset looks compressed:

library(flowStats)

library(stringr)

require(lattice)

file = "C:/Users/alee/Documents/RPRC Data Management/dag_Alex/Manuscript/LymphGate/Test_Denmark_CCIT_untransformed/"

data <- read.flowSet(path=file, pattern='*.fcs')

lg <- lymphGate(data, channels=c("CD4_APC-A", "CD3_BDHorizonV450-A"), preselection = NULL,

scale = 1.0)

xyplot(`CD4_APC-A`~`CD3_BDHorizonV450-A`, transform(data[[1]], `CD4_APC-A`=(`CD4_APC-A`/32767)*200, `CD3_BDHorizonV450-A`=(`CD3_BDHorizonV450-A`/32767)*200))

Thank you