'4096' is the value stored in '$PnR' keyword from `FCS TEXT` segment. In order to find out why it is this value, you need to go back to the instrument where the FCS is generated. In terms of actual data value, I don't see any problem with it.
> library(flowCore) > fr <- read.FCS("~/20150713_R1_CyFlow.fcs") > fr flowFrame object '20150713_R1_CyFlow.fcs' with 1107833 cells and 4 observables: name desc range minRange maxRange $P1 FSC FSC-UV 4096 1.000225 10000 $P2 SSC SSC-UV 4096 1.000225 10000 $P3 FL1 FL4-UV 4096 1.000225 10000 $P4 Time - 4096 0.000000 4095 107 keywords are stored in the 'description' slot > apply(exprs(fr),2, range) FSC SSC FL1 Time [1,] 1.000 1.000 1.000 0 [2,] 9977.539 9977.539 9977.539 4095
On 07/29/2016 03:47 AM, Joachim Schumann wrote:
just one question concerning the read.FCS method. I think that the method is not showing the real raw fcs data, the measured value of all channels for each cell, because the range is from 0-4095. But at the Software Summit the scale ranges from 10^0 to 10^4 which is 1-10.000. Is there any way to extract the real raw data of the fcs file? Or are the values given by the read.FCS method the real ones?
I used he following code:
-- M. Sc. Joachim Schumann PhD Student Department of Environmental Microbiology AG Flow Cytometry Helmholtz Centre for Environmental Research - UFZ Permoserstraße 15, 04318 Leipzig Tel.: 0049-341-235-1330 E-Mail: email@example.com http://www.ufz.de