flowCore: uneven number of tokens / The last keyword is dropped.
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OT • 0
@ot-9575
Last seen 10 months ago
Germany

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
flowCore • 1.0k views
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suppressWarnings(read.FCS("test.fcs", emptyValue=FALSE))
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Thank you for the suggestion. suppressWarnings() doesn't do it here, because these aren't actually warnings, but sink("/dev/null") takes cares of it.

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SamGG ▴ 270
@samgg-6428
Last seen 8 weeks ago
France/Marseille/Inserm

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.

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(empty comment, sorry)

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Dear @SamGG, thanks for this wonderful web validators! Are there any R package that can perform this validation but via terminal without web needed?

Thanks again!

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Hi,

Zach's solution is pure Javascript.

flowIO is R based. The source code is available at https://bitbucket.org/Mira_Koblizek/flowio/src/master/

The Shiny application is based on functions that are available separately (see the R folder). There is a R markdown script that seems to check every parts of the FCS. So you can get easily a nicely formatted document. The shiny app sounds to refer to this Rmd file for the reporting. The interactive part of flowIO concerns mainly changing values. https://bitbucket.org/MiraKoblizek/flowio/src/master/inst/shiny/app.R https://bitbucket.org/MiraKoblizek/flowio/src/master/inst/shiny/checks.Rmd

Thanks to those authors for this interesting application and for having designed it wisely. Contact them directly to get more information/feedback. Please share your developments with the community.

Best.

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