FCS parse text error

[Bunmi0616]

Hello,

I am trying to run an analysis with files that were generated using the new XT platform for the Helios for CyTOF. I am getting this error message: Error in fcsTextParse: Empty keyword name detected. Is there a way around this?

Kind regards, Bunmi

[Bunmi0616]

Heres a copy of the exact error message:

The name provided ('hand-o-right') is deprecated in Font Awesome 5:

• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('repeat') is deprecated in Font Awesome 5:
• please consider using 'redo' or 'fas fa-redo' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('area-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-area' or 'fas fa-chart-area' instead
• use the verify_fa = FALSE to deactivate these messages Warning: Good news! You don't need to call useShinyalert() anymore. Please remove this line from your code. If you really want to pre-load {shinyalert} to the UI for any reason, use: useShinyalert(force = TRUE) data.table 1.14.2 using 1 threads (see ?getDTthreads). Latest news: r-datatable.com

  ---

  This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode. This is a Mac. Please read https://mac.r-project.org/openmp/. Please engage with Apple and ask them for support. Check r-datatable.com for updates, and our Mac instructions here: https://github.com/Rdatatable/data.table/wiki/Installation. After several years of many reports of installation problems on Mac, it's time to gingerly point out that there have been no similar problems on Windows or Linux.

  ---

Attaching package: ‘data.table’

The following objects are masked from ‘package:reshape2’:

dcast, melt

The name provided ('hand-o-right') is deprecated in Font Awesome 5:

• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('repeat') is deprecated in Font Awesome 5:
• please consider using 'redo' or 'fas fa-redo' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages The name provided ('hand-o-right') is deprecated in Font Awesome 5:
• please consider using 'hand-point-right' or 'fas fa-hand-point-right' instead
• use the verify_fa = FALSE to deactivate these messages This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE This Font Awesome icon ('hand-pointer-o') does not exist:
• if providing a custom html_dependency these name checks can be deactivated with verify_fa = FALSE The name provided ('area-chart') is deprecated in Font Awesome 5:
• please consider using 'chart-area' or 'fas fa-chart-area' instead
• use the verify_fa = FALSE to deactivate these messages Warning: Good news! You don't need to call useShinyalert() anymore. Please remove this line from your code. If you really want to pre-load {shinyalert} to the UI for any reason, use: useShinyalert(force = TRUE) Warning: package ‘flowCore’ was built under R version 4.1.1

Attaching package: ‘flowCore’

The following object is masked from ‘package:VGAM’:

exponential

Warning: Error in fcsTextParse: Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again! [No stack trace available]

[raman91]

Hi @Bunmi0616, you may refer to this issue : https://github.com/nolanlab/spade/issues/134 and see if it helps. It looks like your FCS file header is corrupt because of an empty keyword or incorrectly escaped delimiter. Pls let us know if you need more help. Thank you

[Bunmi0616]

Hi @raman91, I tried the following variations of the suggested code in[ nolanlab/spade#134] and still getting the same error message as above. After loading the necessary libraries: