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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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How to filter out high-intensity events for a marker for multiple FCS files? #329

Closed denvercal1234GitHub closed 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

I hope to use the package to perform clustering of my spectral flow data, but I would like to first remove all events across all FCS files that have intensity greater than 2x10^6 for all markers, because they skewed my clusters.

My input = compensated, untransformed FCS.

I tried to use PeacoQC::RemoveMargins() as below (also in https://github.com/saeyslab/PeacoQC/issues/19), but it has not worked.

Does CATALYST have some function to do this?

Thank you for your help!

TRIAL_fcs_data <- read.flowSet(path=".../FCS/FCS_trial", pattern="*.fcs", transformation = FALSE, truncate_max_range = FALSE) #fcs_data will be a FlowSet object

channels <- c("FJComp-AF-A", 
              "FJComp-AF594-A", 
              "FJComp-APC-A",
              "FJComp-APC-Fire 750-A")

channelSpecs <- list(
              "FJComp-AF-A" = list(minRange = 0, maxRange = 2000000), 
              "FJComp-AF594-A"= list(minRange = 0, maxRange = 2000000), 
              "FJComp-APC-A"= list(minRange = 0, maxRange = 2000000),
              "FJComp-APC-Fire 750-A"= list(minRange = 0, maxRange = 2000000))

for (i in 1:length(TRIAL_fcs_data )){
    # Remove margins
  print(i)
    F37_CD4CD8DP_Untransformed_TRIAL_fcs_data[[i]] <- PeacoQC::RemoveMargins(ff=F37_CD4CD8DP_Untransformed_TRIAL_fcs_data[[i]], channels=channels, channel_specifications = channelSpecs, output="full")
    print("next")
}

Error:

Warning: provided 66 variables to replace 2 variablesWarning: More than 100 % is considered as a margin event in file F37_10D_CD4_8Adj_KIR2DL1S5_PE.fcs . This should be verified.Warning: no non-missing arguments to min; returning InfWarning: no non-missing arguments to max; returning -InfError in `[[<-`(`*tmp*`, i, value = PeacoQC::RemoveMargins(ff = F37_CD4CD8DP_Untransformed_TRIAL_fcs_data[[i]],  : 
  [[<- defined for objects of type "S4" only for subclasses of environment
> session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.2.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2023-03-07
 rstudio  2022.12.0+353 Elsbeth Geranium (desktop)
 pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version     date (UTC) lib source
 abind                  1.4-5       2016-07-21 [2] CRAN (R 4.2.0)
 askpass                1.1         2019-01-13 [2] CRAN (R 4.2.0)
 backports              1.4.1       2021-12-13 [2] CRAN (R 4.2.0)
 beachmat               2.12.0      2022-04-26 [1] Bioconductor
 beeswarm               0.4.0       2021-06-01 [1] CRAN (R 4.2.0)
 Biobase              * 2.58.0      2022-11-07 [1] Bioconductor
 BiocGenerics         * 0.44.0      2022-11-07 [1] Bioconductor
 BiocManager            1.30.20     2023-02-24 [1] CRAN (R 4.2.0)
 BiocNeighbors          1.14.0      2022-04-26 [1] Bioconductor
 BiocParallel           1.30.4      2022-10-11 [1] Bioconductor
 BiocSingular           1.12.0      2022-04-26 [1] Bioconductor
 bitops                 1.0-7       2021-04-24 [2] CRAN (R 4.2.0)
 broom                  1.0.3       2023-01-25 [2] CRAN (R 4.2.0)
 bslib                  0.4.2       2022-12-16 [2] CRAN (R 4.2.0)
 cachem                 1.0.7       2023-02-24 [1] CRAN (R 4.2.2)
 callr                  3.7.3       2022-11-02 [2] CRAN (R 4.2.1)
 car                    3.1-1       2022-10-19 [2] CRAN (R 4.2.0)
 carData                3.0-5       2022-01-06 [2] CRAN (R 4.2.0)
 caret                * 6.0-93      2022-08-09 [2] CRAN (R 4.2.0)
 CATALYST             * 1.20.1      2022-05-22 [1] Bioconductor
 changepoint            2.2.4       2022-11-03 [1] CRAN (R 4.2.0)
 circlize               0.4.15      2022-05-10 [1] CRAN (R 4.2.0)
 class                * 7.3-21      2023-01-23 [2] CRAN (R 4.2.0)
 cli                    3.6.0       2023-01-09 [2] CRAN (R 4.2.0)
 clue                   0.3-64      2023-01-31 [2] CRAN (R 4.2.0)
 cluster                2.1.4       2022-08-22 [2] CRAN (R 4.2.2)
 codetools              0.2-19      2023-02-01 [2] CRAN (R 4.2.0)
 colorRamps           * 2.3.1       2022-05-02 [2] CRAN (R 4.2.0)
 colorspace             2.1-0       2023-01-23 [2] CRAN (R 4.2.0)
 ComplexHeatmap         2.14.0      2022-11-07 [1] Bioconductor
 ConsensusClusterPlus   1.62.0      2022-11-07 [1] Bioconductor
 corpcor                1.6.10      2021-09-16 [2] CRAN (R 4.2.0)
 cowplot                1.1.1       2020-12-30 [2] CRAN (R 4.2.0)
 crayon                 1.5.2       2022-09-29 [2] CRAN (R 4.2.0)
 curl                   5.0.0       2023-01-12 [2] CRAN (R 4.2.0)
 cytolib                2.10.1      2023-01-23 [1] Bioconductor
 CytoNorm             * 0.0.10      2023-01-18 [1] Github (saeyslab/CytoNorm@166f9ff)
 data.table           * 1.14.8      2023-02-17 [2] CRAN (R 4.2.0)
 DBI                    1.1.3       2022-06-18 [2] CRAN (R 4.2.0)
 DelayedArray           0.24.0      2022-11-07 [1] Bioconductor
 DelayedMatrixStats     1.18.2      2022-10-13 [1] Bioconductor
 deldir                 1.0-6       2021-10-23 [2] CRAN (R 4.2.0)
 DEoptimR               1.0-11      2022-04-03 [2] CRAN (R 4.2.0)
 deSolve                1.34        2022-10-22 [2] CRAN (R 4.2.0)
 devtools             * 2.4.5       2022-10-11 [1] CRAN (R 4.2.0)
 digest                 0.6.31      2022-12-11 [2] CRAN (R 4.2.0)
 doParallel             1.0.17      2022-02-07 [2] CRAN (R 4.2.0)
 dplyr                * 1.1.0       2023-01-29 [1] CRAN (R 4.2.0)
 drc                    3.0-1       2016-08-30 [1] CRAN (R 4.2.0)
 e1071                  1.7-13      2023-02-01 [2] CRAN (R 4.2.0)
 ellipsis               0.3.2       2021-04-29 [2] CRAN (R 4.2.0)
 evaluate               0.20        2023-01-17 [2] CRAN (R 4.2.0)
 fansi                  1.0.4       2023-01-22 [2] CRAN (R 4.2.0)
 farver                 2.1.1       2022-07-06 [2] CRAN (R 4.2.0)
 fastmap                1.1.1       2023-02-24 [1] CRAN (R 4.2.0)
 fda                    6.0.5       2022-07-04 [2] CRAN (R 4.2.0)
 fds                    1.8         2018-10-31 [2] CRAN (R 4.2.0)
 fitdistrplus           1.1-8       2022-03-10 [2] CRAN (R 4.2.0)
 flowAI               * 1.26.0      2022-04-26 [1] Bioconductor
 flowCore             * 2.10.0      2022-11-07 [1] Bioconductor
 FlowSOM              * 2.6.0       2022-11-07 [1] Bioconductor
 flowStats            * 4.8.2       2022-07-12 [2] Bioconductor
 flowViz              * 1.62.0      2022-11-07 [1] Bioconductor
 flowVS               * 1.28.0      2022-04-26 [1] Bioconductor
 flowWorkspace          4.10.1      2023-01-01 [1] Bioconductor
 foreach                1.5.2       2022-02-02 [2] CRAN (R 4.2.0)
 fs                     1.6.1       2023-02-06 [2] CRAN (R 4.2.0)
 future                 1.31.0      2023-02-01 [2] CRAN (R 4.2.0)
 future.apply           1.10.0      2022-11-05 [2] CRAN (R 4.2.1)
 generics               0.1.3       2022-07-05 [2] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.9      2023-02-02 [1] Bioconductor
 GenomeInfoDbData       1.2.9       2023-01-16 [1] Bioconductor
 GenomicRanges        * 1.50.2      2022-12-18 [1] Bioconductor
 GetoptLong             1.0.5       2020-12-15 [1] CRAN (R 4.2.0)
 ggbeeswarm             0.7.1       2022-12-16 [1] CRAN (R 4.2.0)
 ggforce                0.4.1       2022-10-04 [2] CRAN (R 4.2.0)
 ggnewscale             0.4.8       2022-10-06 [2] CRAN (R 4.2.0)
 ggplot2              * 3.4.1       2023-02-10 [1] CRAN (R 4.2.0)
 ggpointdensity       * 0.1.0       2019-08-28 [2] CRAN (R 4.2.0)
 ggpubr               * 0.6.0       2023-02-10 [2] CRAN (R 4.2.0)
 ggrepel                0.9.3       2023-02-03 [2] CRAN (R 4.2.0)
 ggridges               0.5.4       2022-09-26 [2] CRAN (R 4.2.0)
 ggsignif               0.6.4       2022-10-13 [2] CRAN (R 4.2.0)
 ggthemes             * 4.2.4       2021-01-20 [2] CRAN (R 4.2.0)
 glmnet                 4.1-6       2022-11-27 [1] CRAN (R 4.2.0)
 glmnetUtils            1.1.8       2021-02-25 [1] CRAN (R 4.2.0)
 GlobalOptions          0.1.2       2020-06-10 [1] CRAN (R 4.2.0)
 globals                0.16.2      2022-11-21 [2] CRAN (R 4.2.2)
 glue                   1.6.2       2022-02-24 [2] CRAN (R 4.2.0)
 goftest                1.2-3       2021-10-07 [2] CRAN (R 4.2.0)
 gower                  1.0.1       2022-12-22 [2] CRAN (R 4.2.0)
 graph                  1.76.0      2022-11-07 [1] Bioconductor
 gridExtra            * 2.3         2017-09-09 [2] CRAN (R 4.2.0)
 gtable                 0.3.1       2022-09-01 [2] CRAN (R 4.2.0)
 gtools                 3.9.4       2022-11-27 [2] CRAN (R 4.2.2)
 hardhat                1.2.0       2022-06-30 [2] CRAN (R 4.2.0)
 hdrcde                 3.4         2021-01-18 [2] CRAN (R 4.2.0)
 hexbin                 1.28.2      2021-01-08 [2] CRAN (R 4.2.0)
 highr                  0.10        2022-12-22 [2] CRAN (R 4.2.0)
 htmltools              0.5.4       2022-12-07 [2] CRAN (R 4.2.0)
 htmlwidgets            1.6.1       2023-01-07 [2] CRAN (R 4.2.0)
 httpuv                 1.6.9       2023-02-14 [2] CRAN (R 4.2.0)
 httr                   1.4.5       2023-02-24 [1] CRAN (R 4.2.2)
 ica                    1.0-3       2022-07-08 [2] CRAN (R 4.2.0)
 IDPmisc                1.1.20      2020-01-21 [2] CRAN (R 4.2.0)
 igraph               * 1.4.1       2023-02-24 [1] CRAN (R 4.2.0)
 infinityFlow         * 1.6.0       2022-04-26 [1] Bioconductor
 interp                 1.1-3       2022-07-13 [2] CRAN (R 4.2.0)
 ipred                  0.9-13      2022-06-02 [2] CRAN (R 4.2.0)
 IRanges              * 2.32.0      2022-11-07 [1] Bioconductor
 irlba                  2.3.5.1     2022-10-03 [2] CRAN (R 4.2.0)
 iterators              1.0.14      2022-02-05 [2] CRAN (R 4.2.0)
 jpeg                   0.1-10      2022-11-29 [2] CRAN (R 4.2.0)
 jquerylib              0.1.4       2021-04-26 [2] CRAN (R 4.2.0)
 jsonlite               1.8.4       2022-12-06 [2] CRAN (R 4.2.0)
 KernSmooth             2.23-20     2021-05-03 [2] CRAN (R 4.2.2)
 knitr                * 1.42        2023-01-25 [1] CRAN (R 4.2.2)
 ks                     1.14.0      2022-11-24 [2] CRAN (R 4.2.2)
 later                  1.3.0       2021-08-18 [2] CRAN (R 4.2.0)
 lattice              * 0.20-45     2021-09-22 [2] CRAN (R 4.2.2)
 latticeExtra           0.6-30      2022-07-04 [2] CRAN (R 4.2.0)
 lava                   1.7.2.1     2023-02-27 [2] CRAN (R 4.2.0)
 lazyeval               0.2.2       2019-03-15 [2] CRAN (R 4.2.0)
 leiden                 0.4.3       2022-09-10 [2] CRAN (R 4.2.0)
 lifecycle              1.0.3.9000  2022-10-17 [2] Github (r-lib/lifecycle@80a1e52)
 listenv                0.9.0       2022-12-16 [2] CRAN (R 4.2.0)
 lmtest                 0.9-40      2022-03-21 [2] CRAN (R 4.2.0)
 lubridate              1.9.2       2023-02-10 [2] CRAN (R 4.2.0)
 magrittr               2.0.3       2022-03-30 [2] CRAN (R 4.2.0)
 MASS                   7.3-58.2    2023-01-23 [1] CRAN (R 4.2.0)
 matlab                 1.0.4       2022-06-01 [1] CRAN (R 4.2.0)
 Matrix               * 1.5-3       2022-11-11 [1] CRAN (R 4.2.1)
 MatrixGenerics       * 1.10.0      2022-11-07 [1] Bioconductor
 matrixStats          * 0.63.0      2022-11-18 [2] CRAN (R 4.2.0)
 mclust                 6.0.0       2022-10-31 [2] CRAN (R 4.2.0)
 memoise                2.0.1       2021-11-26 [2] CRAN (R 4.2.0)
 mime                   0.12        2021-09-28 [2] CRAN (R 4.2.0)
 miniUI                 0.1.1.1     2018-05-18 [2] CRAN (R 4.2.0)
 mnormt                 2.1.1       2022-09-26 [2] CRAN (R 4.2.0)
 ModelMetrics           1.2.2.2     2020-03-17 [2] CRAN (R 4.2.0)
 multcomp               1.4-22      2023-02-10 [1] CRAN (R 4.2.0)
 munsell                0.5.0       2018-06-12 [2] CRAN (R 4.2.0)
 mvtnorm                1.1-3       2021-10-08 [2] CRAN (R 4.2.0)
 ncdfFlow               2.44.0      2022-11-07 [1] Bioconductor
 nlme                   3.1-162     2023-01-31 [2] CRAN (R 4.2.0)
 nnet                   7.3-18      2022-09-28 [2] CRAN (R 4.2.2)
 nnls                   1.4         2012-03-19 [1] CRAN (R 4.2.0)
 openssl                2.0.5       2022-12-06 [2] CRAN (R 4.2.0)
 parallelly             1.34.0      2023-01-13 [2] CRAN (R 4.2.0)
 patchwork              1.1.2.9000  2023-01-28 [1] Github (thomasp85/patchwork@c14c960)
 pbapply                1.7-0       2023-01-13 [1] CRAN (R 4.2.0)
 pcaPP                  2.0-3       2022-10-24 [2] CRAN (R 4.2.1)
 PeacoQC              * 1.9.3       2023-02-06 [1] Github (saeyslab/PeacoQC@64c84ad)
 pheatmap             * 1.0.12      2019-01-04 [2] CRAN (R 4.2.0)
 pillar                 1.8.1       2022-08-19 [2] CRAN (R 4.2.0)
 pkgbuild               1.4.0       2022-11-27 [2] CRAN (R 4.2.2)
 pkgconfig              2.0.3       2019-09-22 [2] CRAN (R 4.2.0)
 pkgload                1.3.2       2022-11-16 [2] CRAN (R 4.2.0)
 plotly                 4.10.1.9000 2023-02-28 [1] Github (plotly/plotly.R@9ee5480)
 plotrix                3.8-2       2021-09-08 [1] CRAN (R 4.2.0)
 plyr                 * 1.8.8       2022-11-11 [2] CRAN (R 4.2.1)
 png                    0.1-8       2022-11-29 [2] CRAN (R 4.2.0)
 polyclip               1.10-4      2022-10-20 [2] CRAN (R 4.2.0)
 pracma                 2.4.2       2022-09-22 [2] CRAN (R 4.2.0)
 prettyunits            1.1.1       2020-01-24 [2] CRAN (R 4.2.0)
 pROC                   1.18.0      2021-09-03 [2] CRAN (R 4.2.0)
 processx               3.8.0       2022-10-26 [2] CRAN (R 4.2.0)
 prodlim                2019.11.13  2019-11-17 [2] CRAN (R 4.2.0)
 profvis                0.3.7       2020-11-02 [2] CRAN (R 4.2.0)
 progressr              0.13.0      2023-01-10 [2] CRAN (R 4.2.0)
 promises               1.2.0.1     2021-02-11 [2] CRAN (R 4.2.0)
 proxy                  0.4-27      2022-06-09 [2] CRAN (R 4.2.0)
 ps                     1.7.2       2022-10-26 [2] CRAN (R 4.2.0)
 purrr                  1.0.1       2023-01-10 [2] CRAN (R 4.2.0)
 R6                     2.5.1       2021-08-19 [2] CRAN (R 4.2.0)
 rainbow                3.7         2022-10-09 [2] CRAN (R 4.2.0)
 RANN                   2.6.1       2019-01-08 [2] CRAN (R 4.2.0)
 raster                 3.6-20      2023-03-06 [1] CRAN (R 4.2.2)
 RColorBrewer         * 1.1-3       2022-04-03 [2] CRAN (R 4.2.0)
 Rcpp                   1.0.10      2023-01-22 [2] CRAN (R 4.2.0)
 RcppAnnoy              0.0.20      2022-10-27 [2] CRAN (R 4.2.1)
 RCurl                  1.98-1.10   2023-01-27 [2] CRAN (R 4.2.0)
 recipes                1.0.5       2023-02-20 [2] CRAN (R 4.2.0)
 remotes                2.4.2       2021-11-30 [1] CRAN (R 4.2.0)
 reshape2               1.4.4       2020-04-09 [2] CRAN (R 4.2.0)
 reticulate           * 1.28        2023-01-27 [2] CRAN (R 4.2.0)
 Rgraphviz              2.42.0      2022-11-07 [1] Bioconductor
 rJava                  1.0-6       2021-12-10 [1] CRAN (R 4.2.0)
 rjson                  0.2.21      2022-01-09 [1] CRAN (R 4.2.0)
 rlang                  1.0.6       2022-09-24 [2] CRAN (R 4.2.0)
 rmarkdown              2.20        2023-01-19 [2] CRAN (R 4.2.0)
 robustbase             0.95-0      2022-04-02 [2] CRAN (R 4.2.0)
 ROCR                   1.0-11      2020-05-02 [2] CRAN (R 4.2.0)
 rpart                  4.1.19      2022-10-21 [2] CRAN (R 4.2.2)
 RProtoBufLib           2.10.0      2022-11-07 [1] Bioconductor
 rrcov                  1.7-2       2022-10-24 [2] CRAN (R 4.2.1)
 RSpectra               0.16-1      2022-04-24 [2] CRAN (R 4.2.0)
 rstatix                0.7.2       2023-02-01 [2] CRAN (R 4.2.0)
 rstudioapi           * 0.14        2022-08-22 [2] CRAN (R 4.2.0)
 rsvd                   1.0.5       2021-04-16 [2] CRAN (R 4.2.0)
 Rtsne                * 0.16        2022-04-17 [2] CRAN (R 4.2.0)
 S4Vectors            * 0.36.1      2022-12-07 [1] Bioconductor
 sandwich               3.0-2       2022-06-15 [1] CRAN (R 4.2.0)
 sass                   0.4.5       2023-01-24 [2] CRAN (R 4.2.0)
 ScaledMatrix           1.4.1       2022-09-11 [1] Bioconductor
 scales               * 1.2.1       2022-08-20 [2] CRAN (R 4.2.0)
 scater                 1.24.0      2022-04-26 [1] Bioconductor
 scattermore            0.8         2022-02-14 [2] CRAN (R 4.2.0)
 sctransform            0.3.5.9002  2023-02-06 [1] Github (satijalab/sctransform@02dddee)
 scuttle                1.6.3       2022-08-23 [1] Bioconductor
 sessioninfo            1.2.2       2021-12-06 [2] CRAN (R 4.2.0)
 Seurat                 4.3.0.9001  2023-02-28 [1] Github (satijalab/seurat@54e2fe5)
 SeuratObject           4.1.3       2022-11-07 [2] CRAN (R 4.2.1)
 shape                  1.4.6       2021-05-19 [1] CRAN (R 4.2.0)
 shiny                  1.7.4       2022-12-15 [2] CRAN (R 4.2.0)
 SingleCellExperiment * 1.20.0      2022-11-07 [1] Bioconductor
 sp                     1.6-0       2023-01-19 [1] CRAN (R 4.2.0)
 sparseMatrixStats      1.8.0       2022-04-26 [1] Bioconductor
 spatstat.data          3.0-0       2022-10-21 [2] CRAN (R 4.2.0)
 spatstat.explore       3.0-6       2023-01-26 [2] CRAN (R 4.2.0)
 spatstat.geom          3.0-6       2023-01-30 [1] CRAN (R 4.2.0)
 spatstat.random        3.1-3       2023-01-25 [2] CRAN (R 4.2.0)
 spatstat.sparse        3.0-0       2022-10-21 [2] CRAN (R 4.2.0)
 spatstat.utils         3.0-1       2022-10-19 [2] CRAN (R 4.2.0)
 Spectre              * 1.0.0-0     2023-02-06 [1] Github (immunedynamics/spectre@9ad31d9)
 stringi                1.7.12      2023-01-11 [2] CRAN (R 4.2.0)
 stringr                1.5.0       2022-12-02 [2] CRAN (R 4.2.0)
 SummarizedExperiment * 1.28.0      2022-11-07 [1] Bioconductor
 survival               3.5-3       2023-02-12 [2] CRAN (R 4.2.2)
 tensor                 1.5         2012-05-05 [2] CRAN (R 4.2.0)
 terra                  1.7-18      2023-03-06 [2] CRAN (R 4.2.0)
 TH.data                1.1-1       2022-04-26 [1] CRAN (R 4.2.0)
 tibble                 3.1.8       2022-07-22 [2] CRAN (R 4.2.0)
 tidyr                * 1.3.0       2023-01-24 [2] CRAN (R 4.2.0)
 tidyselect             1.2.0       2022-10-10 [2] CRAN (R 4.2.1)
 timechange             0.2.0       2023-01-11 [2] CRAN (R 4.2.0)
 timeDate               4022.108    2023-01-07 [2] CRAN (R 4.2.0)
 tweenr                 2.0.2       2022-09-06 [2] CRAN (R 4.2.0)
 umap                 * 0.2.10.0    2023-02-01 [2] CRAN (R 4.2.0)
 urlchecker             1.0.1       2021-11-30 [2] CRAN (R 4.2.0)
 usethis              * 2.1.6       2022-05-25 [2] CRAN (R 4.2.0)
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 [1] /Users/clusteredatom/Library/R/arm64/4.2/library
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SamGG commented 1 year ago

IMHO PeacoQC is the right tool to use. So, you should address your issue to the github of PeacoQC. Issues section of github repositories mainly aims to solve a bug. If you are asking a general question, especially if it could be solved in different ways (PeacoQC, a loop on the FCS files...), you should ask it on the support forum of Bioconductor. Best.

denvercal1234GitHub commented 1 year ago

Thank you, Sam. For anyone having the same Q, it was solved in PeacoQC issue as referenced above.