FlowJo and FlowAI error message troubleshooting
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Entering edit mode
akaw3 • 0
@ecf08b02
Last seen 5 months ago
Netherlands

Here is the latter part of the code but towards the end an error message pops up that teminates the instruction - any suggestions appreciated.....(I only have a basic grasp of R)

```> # The argument second_fractionFR must be greater or equal to timestep.

fcstimestep <- as.numeric(inputFCS@description[['$TIMESTEP']]) if ((length(fcstimestep) > 0) && fj_second_fractionFR < fcstimestep) fj_second_fractionFR <- fcstimestep

newFlowFrame <- flow_auto_qc(

  • inputFCS,
  • output = 2,
  • ChExcludeFS = ChRemoveFS,
  • remove_from = "all",
  • second_fractionFR = fj_second_fractionFR,
  • max_cptFS = 3.0,
  • pen_valueFS = pen_valueFS,
  • outlier_binsFS = FALSE,
  • decompFR = TRUE,
  • sideFM = "both",
  • neg_valuesFM = 1,
  • fcs_QC = FALSE,
  • folder_results = FALSE,
  • html_report = TRUE, ## We extract the figures from this
  • alphaFR = 0.01) Quality control for the file: 180313A PBMC CD127 BV421 Titration_180313A CD127 Titration_Tube 2 4ul 5.24% of anomalous cells detected in the flow rate check. 16.2% of anomalous cells detected in signal acquisition check. 5.68% of anomalous cells detected in the dynamic range check. Error in file(con, "w") : cannot open the connection Calls: flow_auto_qc -> knit2html -> <Anonymous> -> writeLines -> file In addition: Warning messages: 1: In file.create(to[okay]) : cannot create file '180313A PBMC CD127 BV421 Titration_180313A CD127 Titration_Tube 2 4ul_template.Rmd', reason 'No such file or directory' 2: In file(con, "w") : cannot open file '180313A PBMC CD127 BV421 Titration_180313A CD127 Titration_Tube 2 4ulTRUE.html': No such file or directory Execution halted
FlowAI FlowJo • 144 views
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Entering edit mode

solved it - it appears file name length appears to be important.

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