Dear all,

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.

Thank you!

> 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

Hi, This warning arises usually when the file dos not comply to the FCS standard. You could check the compliance with http://bioinformin.cesnet.cz/flowIO/ (flowIO, CLIP, Prague) or https://primitybio.github.io/fcs-validator/ (Zach Bjornson). More on such error in problems with fcs 3.1 files exported from Macsquantify. Best.