[BioC] flowWorkspace transformation on FCS 3 data

[Nikolas]

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