I'm experiencing issues reading FCS 3.2 files that appear to be new to the most recent release of flowCore. Previously, I was able to read in FCS 3.2 file from the A8 or S8 cytometers, with warnings, but successfully. Now, using the same files that I have worked with a few months ago, this fails. If I pass the files through FlowJo first, exporting a new copy, the files can be read into R using read.FCS.

I understand that you do not fully support FCS 3.2. You should, however, be aware of this potential problem.

> fcs.file.original <-list.files( "./FilesToUnmix/SSC", full.names = TRUE )[ 1 ]
> fcs.file.flowjo <- list.files( "./FilesToUnmix/SSC2", full.names = TRUE )[ 1 ]
> fcs.read.test.original <- flowCore::read.FCS( fcs.file.original )
Error in if (any(idx)) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)

> fcs.read.test.flowjo <- flowCore::read.FCS( fcs.file.flowjo )
There were 50 or more warnings (use warnings() to see the first 50)

sessionInfo( )
R version 4.4.3 (2025-02-28 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_4.4.3      RProtoBufLib_2.16.0 cytolib_2.16.0      tools_4.4.3         rstudioapi_0.17.1  
 [6] Biobase_2.64.0      S4Vectors_0.42.1    flowCore_2.16.0     BiocGenerics_0.50.0 matrixStats_1.5.0  
[11] stats4_4.4.3