Hello, I am bit puzzled as to how flowWorkspace transforms FCS 3 data (see code below). I would expect fcs.data.comp and fcs.data.1 to contain similar (if not identical) data yet the range is completely different. Some transform has taken place. Does this have anything to do with flowWorkspace trying to simulate the binning process that FlowJo does on FCS 3 data? Someone at TreeStar told me that FlowJo does binning with 4096 bins which is possibly what is going on here? Many thanks for you help, Niko. library(flowWorkspace) library(flowCore) #CAD61.xml is a flowjo workspace file which references CAD61.fcs openWorkspace("CAD61.xml") -> wsp try(parseWorkspace(wsp, execute=TRUE, isNcdf=FALSE, path=".", name="All Samples")) -> G G at set[[1]]->g getData(g, 1)->fcs.data.1 read.FCS('CAD61.fcs')->fcs.data compensate(fcs.data, fcs.data at description[["SPILL"]])->fcs.data.comp > fcs.data.comp flowFrame object '71d0bf04-ddb1-4284-ad2b-af44322ecdfb' with 300195 cells and 9 observables: name desc range minRange maxRange $P1 FSC-A <na> 262144 0.00 262143 $P2 SSC-A <na> 262144 -111.00 262143 $P3 Alexa-488-A cd127 262144 -111.00 262143 $P4 PE-Cy7-A hladr 262144 -111.00 262143 $P5 APC-A cd25_ma251+2a3 262144 -108.00 262143 $P6 PE-A cd101 262144 -111.00 262143 $P7 Alexa-700-A cd4 262144 -96.00 262143 $P8 Pacific Blue-A cd45ra 262144 -91.64 262143 $P9 Time <na> 262144 0.00 262143 162 keywords are stored in the 'description' slot > fcs.data.1 flowFrame object '71d0bf04-ddb1-4284-ad2b-af44322ecdfb' with 300195 cells and 9 observables: name desc range minRange maxRange $P1 FSC-A <na> 3641.837 455.000000 4096.837 $P2 SSC-A <na> 262254.000 -111.000000 262143.000 $P3 <alexa-488-a> cd127 4098.176 -1.339711 4096.837 $P4 <pe-cy7-a> hladr 4098.176 -1.339711 4096.837 $P5 <apc-a> cd25_ma251+2a3 4088.140 8.696338 4096.837 $P6 <pe-a> cd101 4098.176 -1.339711 4096.837 $P7 <alexa-700-a> cd4 4046.566 50.270760 4096.837 $P8 <pacific blue-a=""> cd45ra 4030.885 65.951978 4096.837 $P9 Time <na> 21737.000 0.000000 21737.000 162 keywords are stored in the 'description' slot