Entering edit mode
I am new to Bioconductor and R so have been playing around with it. I was looking at the logicleTransform() method.
lgcl <- logicleTransform( w = 0.0, t= 262144, m = 4.5, a = 0)
res<-lgcl(200000)
res
The output of this is 4.38249. Then I came across the Javascript implementation (https://github.com/bioturing/logicle-js) and ran the same logicle transform:
var res = api.LogicleTransform([200000], 262144, 4.5, 0, 0)
console.log(res);
But the output of this was 0.9738866831164751. In fact, the Javascript implementation the output is always between 0 and 1 for any input less than 262144.
Does anyone know why there is such a difference?
EDIT: Any more details I can add here to improve chances of an answer? flowCore version I'm using is flowCore_2.2.0
There are two implementations of logicle in flowCore: logicleTransform and logicletGml2.
"Please note that logicletGml2 and logicleTransform are similar transformations; however, the Gating-ML 2.0 compliant logicletGml2 brings "reasonable" data values to the scale of [0,1] while the logicleTransform scales these values to [0,M]."
The js implementation seems to Gating-ML 2.0 compliant.