we have a new Attune flow cytometer. The resulting FCS files produce a warning message when read in via flowCore, regardless of whether the export from the software is performed as FCS3.0 or FCS3.1.
Successful import is only possible when specifying
emptyValue = FALSE in the call to
read.FCS. Even so, a complaint is raised about an uneven number of tokens and the last keyword being dropped (see below). While this does not (as far as I noticed) impact the downstream analysis in any way, it pollutes the output quite severely when reading in samples from a full plate. I am happy to provide an example FCS file by mail, but I do not see a way to upload an attachment.
> library(flowCore) > > read.FCS("test.fcs") Error in fcsTextParse(txt, emptyValue = emptyValue) : Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again! > > read.FCS("test.fcs", emptyValue=FALSE) uneven number of tokens: 333 The last keyword is dropped. uneven number of tokens: 333 The last keyword is dropped. flowFrame object 'test.fcs' with 27776 cells and 13 observables: name desc range minRange maxRange $P1 Time Time 67108864 0 67108863 $P2 FSC-A FSC-A 1048576 0 1048575 $P3 SSC-A SSC-A 1048576 -111 1048575 $P4 BL1-A FITC-A 1048576 -111 1048575 $P5 RL1-A DiD-A 1048576 -111 1048575 $P6 VL1-A Auto-A 1048576 -111 1048575 $P7 FSC-H FSC-H 1048576 0 1048575 $P8 SSC-H SSC-H 1048576 0 1048575 $P9 BL1-H FITC-H 1048576 0 1048575 $P10 RL1-H DiD-H 1048576 0 1048575 $P11 VL1-H Auto-H 1048576 0 1048575 $P12 FSC-W FSC-W 1024 0 1023 $P13 SSC-W SSC-W 1024 0 1023 196 keywords are stored in the 'description' slot