Error in flowCore::read.FCS(): Error in uint2double(splitted, endian == "big") : vector
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Entering edit mode
Rainer • 0
@rainer-24107
Last seen 11 weeks ago
Switzerland

Hi

I get an error, when trying to read an fps file, where I have no idea what is happening.have posted the .fcs files here https://drive.google.com/drive/folders/1rc_XI_oR-SlhIEIgi4xxdgbGTsAdUIm3 as I have't seen any possibility to attach them to the post.

I assume, the this is caused by the point, that no particles were detected in for example G12 - as the others have the same size, this is likely the case for these as well

Is there any fix for this? In the original script, I am using readFlowset().

Here is the output:


> read.FCS("G12.fcs", transformation = F);
Error in uint2double(splitted, endian == "big") : vector
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] flowCore_2.4.0                        LEEF.measurement.flowcytometer_0.8.11 testthat_3.1.0                       

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.1    remotes_2.4.0       purrr_0.3.4         vctrs_0.3.8         generics_0.1.1      usethis_2.1.2      
 [7] stats4_4.1.1        yaml_2.2.1          utf8_1.2.2          rlang_0.4.12        pkgbuild_1.2.0      R.oo_1.24.0        
[13] pillar_1.6.4        glue_1.4.2          withr_2.4.2         DBI_1.1.1           R.utils_2.10.1      BiocGenerics_0.38.0
[19] sessioninfo_1.1.1   matrixStats_0.60.0  lifecycle_1.0.1     plyr_1.8.6          RProtoBufLib_2.4.0  cytolib_2.4.0      
[25] R.methodsS3_1.8.1   devtools_2.4.2      memoise_2.0.0       Biobase_2.52.0      callr_3.7.0         fastmap_1.1.0      
[31] ps_1.6.0            parallel_4.1.1      fansi_0.5.0         Rcpp_1.0.7          cachem_1.0.5        S4Vectors_0.30.0   
[37] desc_1.4.0          pkgload_1.2.3       RcppParallel_5.1.4  fs_1.5.0            tiff_0.1-8          processx_3.5.2     
[43] dplyr_1.0.7         rprojroot_2.0.2     cli_3.0.1           tools_4.1.1         magrittr_2.0.1      tibble_3.1.5       
[49] crayon_1.4.1        tidyr_1.1.4         pkgconfig_2.0.3     ellipsis_0.3.2      prettyunits_1.1.1   assertthat_0.2.1   
[55] rstudioapi_0.13     R6_2.5.1            loggit_2.1.1        compiler_4.1.1
read.FCS flowCore • 125 views
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Entering edit mode

I upgraded to BiocManager 3.14 (flowCore version 2.6.0) and still the same error.

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