Describe the bug
I can use the method exprs on a cytoframe
To Reproduce
dataDir <- system.file("extdata",package="flowWorkspaceData")
files <- list.files(dataDir, "Cyto", full.names = TRUE)
library(flowWorkspace)
#> As part of improvements to flowWorkspace, some behavior of
#> GatingSet objects has changed. For details, please read the section
#> titled "The cytoframe and cytoset classes" in the package vignette:
#>
#> vignette("flowWorkspace-Introduction", "flowWorkspace")
cf <- load_cytoframe_from_fcs(files[1], num_threads = 4)
cf
#> cytoframe object 'CytoTrol_CytoTrol_1.fcs'
#> with 119531 cells and 12 observables:
#> name desc range minRange maxRange
#> $P1 FSC-A NA 262143 0 262143
#> $P2 FSC-H NA 262143 0 262143
#> $P3 FSC-W NA 262143 0 262143
#> $P4 SSC-A NA 262143 0 262143
#> $P5 B710-A CD4 PcpCy55 262143 -111 262143
#> ... ... ... ... ... ...
#> $P8 V450-A CD3 V450 262143 -111 262143
#> $P9 V545-A HLA-DR V500 262143 -111 262143
#> $P10 G560-A CCR7 PE 262143 -111 262143
#> $P11 G780-A CD45RA PECy7 262143 -111 262143
#> $P12 Time NA 262143 0 262143
#> 199 keywords are stored in the 'description' slot
#> row names(0):
exprs(cf)
#> Error in `exprs()`:
#> ! could not find function "exprs"
sessionInfo()
#> R version 4.5.2 (2025-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 26200)
#>
#> Matrix products: default
#> LAPACK version 3.12.1
#>
#> locale:
#> [1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8
#> [3] LC_MONETARY=French_France.utf8 LC_NUMERIC=C
#> [5] LC_TIME=French_France.utf8
#>
#> time zone: Europe/Paris
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] flowWorkspace_4.22.1
#>
#> loaded via a namespace (and not attached):
#> [1] Matrix_1.7-4 dplyr_1.2.0 compiler_4.5.2
#> [4] reprex_2.1.1 tidyselect_1.2.1 Biobase_2.70.0
#> [7] cytolib_2.22.0 Rgraphviz_2.54.0 IRanges_2.44.0
#> [10] scales_1.4.0 yaml_2.3.12 fastmap_1.2.0
#> [13] lattice_0.22-9 XVector_0.50.0 R6_2.6.1
#> [16] RProtoBufLib_2.22.0 S4Arrays_1.10.1 generics_0.1.4
#> [19] knitr_1.51 BiocGenerics_0.56.0 XML_3.99-0.22
#> [22] graph_1.88.1 DelayedArray_0.36.0 tibble_3.3.1
#> [25] MatrixGenerics_1.22.0 RColorBrewer_1.1-3 pillar_1.11.1
#> [28] ncdfFlow_2.56.0 rlang_1.1.7 flowCore_2.22.1
#> [31] xfun_0.56 fs_1.6.6 otel_0.2.0
#> [34] SparseArray_1.10.8 cli_3.6.5 withr_3.0.2
#> [37] magrittr_2.0.4 digest_0.6.39 grid_4.5.2
#> [40] rstudioapi_0.18.0 lifecycle_1.0.5 S4Vectors_0.48.0
#> [43] vctrs_0.7.1 evaluate_1.0.5 glue_1.8.0
#> [46] data.table_1.18.2.1 farver_2.1.2 abind_1.4-8
#> [49] stats4_4.5.2 rmarkdown_2.30 matrixStats_1.5.0
#> [52] tools_4.5.2 pkgconfig_2.0.3 htmltools_0.5.9
Created on 2026-04-17 with reprex v2.1.1
Expected behavior
I should view the expression intensities.
Additional context
The previous code is working if flowCore is loaded, but doing so makes me unclear of the underlying transformation: the cytoframe is converted to a flowFrame, then exprs is applied?
Describe the bug
I can use the method exprs on a cytoframe
To Reproduce
Created on 2026-04-17 with reprex v2.1.1
Expected behavior
I should view the expression intensities.
Additional context
The previous code is working if flowCore is loaded, but doing so makes me unclear of the underlying transformation: the cytoframe is converted to a flowFrame, then exprs is applied?