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