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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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`sce2fcs`: Error in if (any(idx)) { : missing value where TRUE/FALSE needed, and Warning channel_alias: Multiple channels from one FCS are matched to the same alias! #360

Closed denvercal1234GitHub closed 11 months ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thank you very much for the detailed tutorial.

I attempted to export my sce object back to FCS files for manual gating in FlowJo.

When keep_dr = T, it generated Warning and Error. The warning is due to DR being ran only on a subset of cells and not all cells (https://github.com/HelenaLC/CATALYST/issues/152); however, I am not sure how to fix the Error. 

Warning: $PnR NA is invalid. If it is a numeric string, this could be because it is larger than R's numeric limit: 1.79769313486232e+308. The assigned $PnR value will be imputed from the maximum value of the data in this channel.Warning: 
channel_alias: Multiple channels from one FCS are matched to the same alias!
Integer suffixes added to disambiguate channels.
It is also recommended to verify correct mapping of spillover matrix columns.
Error in if (any(idx)) { : missing value where TRUE/FALSE needed

But, when I set keep_dr = F, the error went away, but new Warning came up.

Would you mind helping me understand this Warning and whether there is certain step I need to do prior to subsequent write.FCS step in the for loop?

(F37_fcs_data_sce_backboneClustering_fs <- CATALYST::sce2fcs(F37_fcs_data_sce_backboneClustering, split_by = "CATALYST30meta14", keep_cd = T, keep_dr = F, assay = "exprs"))
Warning: 
channel_alias: Multiple channels from one FCS are matched to the same alias!
Integer suffixes added to disambiguate channels.
It is also recommended to verify correct mapping of spillover matrix columns.
Warning: 
channel_alias: Multiple channels from one FCS are matched to the same alias!
Integer suffixes added to disambiguate channels.
It is also recommended to verify correct mapping of spillover matrix columns.
....

Thank you for your help. 

> F37_fcs_data_sce_backboneClustering
class: SingleCellExperiment 
dim: 270 4955453 
metadata(5): experiment_info chs_by_fcs cluster_codes SOM_codes delta_area
assays(1): exprs
rownames(270): FSC.A FSC.H ... FlowSOM_cluster_backbone24 FlowSOM_metacluster_backbone24
rowData names(4): channel_name marker_name marker_class used_for_clustering
colnames: NULL
colData names(9): sample_id cell_count_prePeacoQC ... cluster_id CATALYST30meta14
reducedDimNames(2): UMAP TSNE
mainExpName: NULL
altExpNames(0):

> colData(F37_fcs_data_sce_backboneClustering)
DataFrame with 4955453 rows and 9 columns

> reducedDims(F37_fcs_data_sce_backboneClustering)
List of length 2
names(2): UMAP TSNE

> assayNames(F37_fcs_data_sce_backboneClustering)
[1] "exprs"
> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.3 (2023-03-15)
 os       macOS Ventura 13.4.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2023-08-03
 rstudio  2023.06.0+421 Mountain Hydrangea (desktop)
 pandoc   3.1.1 @ /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 [1] CRAN (R 4.2.0)
 askpass                1.1        2019-01-13 [1] CRAN (R 4.2.0)
 backports              1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
 beachmat               2.14.2     2023-04-09 [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            1.30.21.1  2023-07-18 [1] CRAN (R 4.2.0)
 BiocNeighbors          1.16.0     2022-11-07 [1] Bioconductor
 BiocParallel         * 1.32.6     2023-03-19 [1] Bioconductor
 BiocSingular           1.14.0     2022-11-07 [1] Bioconductor
 bitops                 1.0-7      2021-04-24 [1] CRAN (R 4.2.0)
 bluster              * 1.8.0      2022-11-07 [1] Bioconductor
 boot                   1.3-28.1   2022-11-22 [1] CRAN (R 4.2.3)
 broom                  1.0.5      2023-06-09 [1] CRAN (R 4.2.0)
 bslib                  0.5.0      2023-06-09 [1] CRAN (R 4.2.0)
 cachem                 1.0.8      2023-05-01 [1] CRAN (R 4.2.3)
 callr                  3.7.3      2022-11-02 [1] CRAN (R 4.2.0)
 car                    3.1-2      2023-03-30 [1] CRAN (R 4.2.0)
 carData                3.0-5      2022-01-06 [1] CRAN (R 4.2.0)
 caret                * 6.0-94     2023-03-21 [1] CRAN (R 4.2.0)
 CATALYST             * 1.22.0     2022-11-07 [1] Bioconductor
 cellranger             1.1.0      2016-07-27 [1] CRAN (R 4.2.0)
 circlize               0.4.15     2022-05-10 [1] CRAN (R 4.2.0)
 class                * 7.3-22     2023-05-03 [1] CRAN (R 4.2.3)
 cli                    3.6.1      2023-03-23 [1] CRAN (R 4.2.0)
 clue                   0.3-64     2023-01-31 [1] CRAN (R 4.2.0)
 cluster                2.1.4      2022-08-22 [1] CRAN (R 4.2.3)
 codetools              0.2-19     2023-02-01 [1] CRAN (R 4.2.3)
 colorRamps           * 2.3.1      2022-05-02 [1] CRAN (R 4.2.0)
 colorspace             2.1-0      2023-01-23 [1] CRAN (R 4.2.0)
 ComplexHeatmap       * 2.15.4     2023-05-04 [1] Github (jokergoo/ComplexHeatmap@ae0ec42)
 ConsensusClusterPlus   1.62.0     2022-11-07 [1] Bioconductor
 cowplot                1.1.1      2020-12-30 [1] CRAN (R 4.2.0)
 crayon                 1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
 crul                   1.4.0      2023-05-17 [1] CRAN (R 4.2.3)
 cubature               2.1.0      2023-06-11 [1] CRAN (R 4.2.0)
 curl                   5.0.1      2023-06-07 [1] CRAN (R 4.2.0)
 cytolib                2.10.1     2023-01-23 [1] Bioconductor
 CytoNorm             * 0.0.15     2023-04-25 [1] Github (saeyslab/CytoNorm@78c6675)
 data.table           * 1.14.8     2023-02-17 [1] CRAN (R 4.2.0)
 DBI                    1.1.3      2022-06-18 [1] CRAN (R 4.2.0)
 DelayedArray           0.24.0     2022-11-07 [1] Bioconductor
 DelayedMatrixStats     1.20.0     2022-12-04 [1] Bioconductor
 deldir                 1.0-9      2023-05-17 [1] CRAN (R 4.2.3)
 dendextend             1.17.1     2023-03-25 [1] CRAN (R 4.2.0)
 devtools             * 2.4.5      2022-10-11 [1] CRAN (R 4.2.0)
 diffcyt                1.18.0     2022-11-07 [1] Bioconductor
 digest                 0.6.33     2023-07-07 [1] CRAN (R 4.2.0)
 doParallel             1.0.17     2022-02-07 [1] CRAN (R 4.2.0)
 dplyr                * 1.1.2      2023-04-20 [1] CRAN (R 4.2.0)
 drc                    3.0-1      2016-08-30 [1] CRAN (R 4.2.0)
 DT                     0.28       2023-05-18 [1] CRAN (R 4.2.3)
 edgeR                  3.40.2     2023-01-22 [1] Bioconductor
 ellipsis               0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
 evaluate               0.21       2023-05-05 [1] CRAN (R 4.2.0)
 evd                    2.3-6.1    2022-07-04 [1] CRAN (R 4.2.0)
 evmix                  2.12       2019-09-03 [1] CRAN (R 4.2.0)
 extrafont              0.19       2023-01-18 [1] CRAN (R 4.2.0)
 extrafontdb            1.0        2012-06-11 [1] CRAN (R 4.2.0)
 fansi                  1.0.4      2023-01-22 [1] CRAN (R 4.2.0)
 farver                 2.1.1      2022-07-06 [1] CRAN (R 4.2.0)
 fastmap                1.1.1      2023-02-24 [1] CRAN (R 4.2.0)
 fitdistrplus           1.1-11     2023-04-25 [1] CRAN (R 4.2.0)
 flowCore             * 2.10.0     2022-11-07 [1] Bioconductor
 FlowSOM              * 2.6.0      2022-11-07 [1] Bioconductor
 flowViz              * 1.62.0     2022-11-07 [1] Bioconductor
 flowWorkspace          4.10.1     2023-01-01 [1] Bioconductor
 fontBitstreamVera      0.1.1      2017-02-01 [1] CRAN (R 4.2.0)
 fontLiberation         0.1.0      2016-10-15 [1] CRAN (R 4.2.0)
 fontquiver             0.2.1      2017-02-01 [1] CRAN (R 4.2.0)
 foreach                1.5.2      2022-02-02 [1] CRAN (R 4.2.0)
 fs                     1.6.3      2023-07-20 [1] CRAN (R 4.2.0)
 future                 1.33.0     2023-07-01 [1] CRAN (R 4.2.0)
 future.apply           1.11.0     2023-05-21 [1] CRAN (R 4.2.3)
 gdtools                0.3.3      2023-03-27 [1] CRAN (R 4.2.0)
 generics               0.1.3      2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.9     2023-02-05 [1] Bioconductor
 GenomeInfoDbData       1.2.9      2023-04-24 [1] Bioconductor
 GenomicRanges        * 1.50.2     2022-12-18 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] CRAN (R 4.2.0)
 gfonts                 0.2.0      2023-01-08 [1] CRAN (R 4.2.0)
 ggalluvial             0.12.5     2023-02-22 [1] CRAN (R 4.2.0)
 ggbeeswarm             0.7.2      2023-04-29 [1] CRAN (R 4.2.0)
 ggforce                0.4.1      2022-10-04 [1] CRAN (R 4.2.0)
 ggnewscale             0.4.9      2023-05-25 [1] CRAN (R 4.2.0)
 ggplot2              * 3.4.2      2023-04-03 [1] CRAN (R 4.2.0)
 ggpointdensity       * 0.1.0      2019-08-28 [1] CRAN (R 4.2.0)
 ggpubr               * 0.6.0      2023-02-10 [1] CRAN (R 4.2.0)
 ggraph                 2.1.0      2022-10-09 [1] CRAN (R 4.2.0)
 ggrepel                0.9.3      2023-02-03 [1] CRAN (R 4.2.0)
 ggridges               0.5.4      2022-09-26 [1] CRAN (R 4.2.0)
 ggsignif               0.6.4      2022-10-13 [1] CRAN (R 4.2.0)
 ggthemes             * 4.2.4      2021-01-20 [1] CRAN (R 4.2.0)
 ggVennDiagram          1.2.2      2022-09-08 [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 [1] CRAN (R 4.2.0)
 glue                   1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
 goftest              * 1.2-3      2021-10-07 [1] CRAN (R 4.2.0)
 gower                  1.0.1      2022-12-22 [1] CRAN (R 4.2.0)
 graph                  1.76.0     2022-11-07 [1] Bioconductor
 graphlayouts           1.0.0      2023-05-01 [1] CRAN (R 4.2.0)
 gridExtra            * 2.3        2017-09-09 [1] CRAN (R 4.2.0)
 gsl                    2.1-8      2023-01-24 [1] CRAN (R 4.2.0)
 gtable                 0.3.3      2023-03-21 [1] CRAN (R 4.2.0)
 gtools                 3.9.4      2022-11-27 [1] CRAN (R 4.2.0)
 hardhat                1.3.0      2023-03-30 [1] CRAN (R 4.2.0)
 hexbin                 1.28.3     2023-03-21 [1] CRAN (R 4.2.0)
 hrbrthemes             0.8.0      2020-03-06 [1] CRAN (R 4.2.0)
 htmltools              0.5.5      2023-03-23 [1] CRAN (R 4.2.0)
 htmlwidgets            1.6.2      2023-03-17 [1] CRAN (R 4.2.0)
 httpcode               0.3.0      2020-04-10 [1] CRAN (R 4.2.0)
 httpuv                 1.6.11     2023-05-11 [1] CRAN (R 4.2.0)
 httr                   1.4.6      2023-05-08 [1] CRAN (R 4.2.0)
 ica                    1.0-3      2022-07-08 [1] CRAN (R 4.2.0)
 IDPmisc                1.1.20     2020-01-21 [1] CRAN (R 4.2.0)
 igraph               * 1.5.0.1    2023-07-23 [1] CRAN (R 4.2.0)
 interp                 1.1-4      2023-03-31 [1] CRAN (R 4.2.0)
 ipred                  0.9-14     2023-03-09 [1] CRAN (R 4.2.0)
 IRanges              * 2.32.0     2022-11-07 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [1] CRAN (R 4.2.0)
 iterators              1.0.14     2022-02-05 [1] CRAN (R 4.2.0)
 jpeg                   0.1-10     2022-11-29 [1] CRAN (R 4.2.0)
 jquerylib              0.1.4      2021-04-26 [1] CRAN (R 4.2.0)
 jsonlite               1.8.7      2023-06-29 [1] CRAN (R 4.2.0)
 KernSmooth             2.23-22    2023-07-10 [1] CRAN (R 4.2.0)
 knitr                * 1.43       2023-05-25 [1] CRAN (R 4.2.0)
 labeling               0.4.2      2020-10-20 [1] CRAN (R 4.2.0)
 later                  1.3.1      2023-05-02 [1] CRAN (R 4.2.0)
 lattice              * 0.21-8     2023-04-05 [1] CRAN (R 4.2.0)
 latticeExtra           0.6-30     2022-07-04 [1] CRAN (R 4.2.0)
 lava                   1.7.2.1    2023-02-27 [1] CRAN (R 4.2.0)
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.2.0)
 leiden                 0.4.3      2022-09-10 [1] CRAN (R 4.2.0)
 lifecycle              1.0.3      2022-10-07 [1] CRAN (R 4.2.0)
 limma                  3.54.2     2023-03-01 [1] Bioconductor
 listenv                0.9.0      2022-12-16 [1] CRAN (R 4.2.0)
 lme4                   1.1-34     2023-07-04 [1] CRAN (R 4.2.0)
 lmtest                 0.9-40     2022-03-21 [1] CRAN (R 4.2.0)
 locfit                 1.5-9.8    2023-06-11 [1] CRAN (R 4.2.0)
 lubridate              1.9.2      2023-02-10 [1] CRAN (R 4.2.0)
 magrittr               2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
 MASS                   7.3-60     2023-05-04 [1] CRAN (R 4.2.3)
 Matrix               * 1.6-0      2023-07-08 [1] CRAN (R 4.2.3)
 MatrixGenerics       * 1.10.0     2022-11-07 [1] Bioconductor
 matrixStats          * 1.0.0      2023-06-02 [1] CRAN (R 4.2.0)
 memoise                2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
 mgcv                   1.9-0      2023-07-11 [1] CRAN (R 4.2.0)
 mime                   0.12       2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                 0.1.1.1    2018-05-18 [1] CRAN (R 4.2.0)
 minqa                  1.2.5      2022-10-19 [1] CRAN (R 4.2.0)
 ModelMetrics           1.2.2.2    2020-03-17 [1] CRAN (R 4.2.0)
 multcomp               1.4-25     2023-06-20 [1] CRAN (R 4.2.0)
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
 mvtnorm                1.2-2      2023-06-08 [1] CRAN (R 4.2.0)
 ncdfFlow               2.44.0     2022-11-07 [1] Bioconductor
 nlme                   3.1-162    2023-01-31 [1] CRAN (R 4.2.3)
 nloptr                 2.0.3      2022-05-26 [1] CRAN (R 4.2.0)
 nnet                   7.3-19     2023-05-03 [1] CRAN (R 4.2.3)
 nnls                   1.4        2012-03-19 [1] CRAN (R 4.2.0)
 openssl                2.1.0      2023-07-15 [1] CRAN (R 4.2.0)
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 patchwork              1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 pbapply                1.7-2      2023-06-27 [1] CRAN (R 4.2.0)
 PeacoQC              * 1.9.3      2023-04-20 [1] Github (saeyslab/PeacoQC@64c84ad)
 permute                0.9-7      2022-01-27 [1] CRAN (R 4.2.0)
 pheatmap             * 1.0.12     2019-01-04 [1] CRAN (R 4.2.0)
 pillar                 1.9.0      2023-03-22 [1] CRAN (R 4.2.0)
 pkgbuild               1.4.2      2023-06-26 [1] CRAN (R 4.2.0)
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
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 png                    0.1-8      2022-11-29 [1] CRAN (R 4.2.0)
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 powerTCR               1.18.0     2022-11-07 [1] Bioconductor
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 R6                     2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
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 RANN                   2.6.1      2019-01-08 [1] CRAN (R 4.2.0)
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 rgdal                  1.6-7      2023-05-31 [1] CRAN (R 4.2.0)
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 Rgraphviz              2.42.0     2022-11-07 [1] Bioconductor
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 RSpectra               0.16-1     2022-04-24 [1] CRAN (R 4.2.0)
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 rstudioapi           * 0.15.0     2023-07-07 [1] CRAN (R 4.2.0)
 rsvd                   1.0.5      2021-04-16 [1] CRAN (R 4.2.0)
 Rtsne                * 0.16       2022-04-17 [1] CRAN (R 4.2.0)
 Rttf2pt1               1.3.12     2023-01-22 [1] CRAN (R 4.2.0)
 RVenn                  1.1.0      2019-07-18 [1] CRAN (R 4.2.0)
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 sandwich               3.0-2      2022-06-15 [1] CRAN (R 4.2.0)
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 ScaledMatrix           1.6.0      2022-11-07 [1] Bioconductor
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 shiny                  1.7.4.1    2023-07-06 [1] CRAN (R 4.2.0)
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 [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
HelenaLC commented 12 months ago

Re reduced dimensions: Yes, so unless you run runDR(..., cells=NULL) (i.e., using all cells), cell embeddings will not be available (NA) for all cells. So you either have to specify cells=NULL, or filter out cells for which reduced dimensions are not available via

dim_red <- reducedDim(sce)
sub <- filterSCE(sce, !is.na(dim_red[, 1]))
sce2fcs(sub, ...)

Re the second issue, I don't know. This looks like it comes from flowCore not CATALYST... So I am not sure whether it is caused by the FCS to SingleCellExperiment to FCS conversion, or is something that's off with the original FCS files...

denvercal1234GitHub commented 11 months ago

Thanks @HelenaLC.

I checked and the second warning of truncation occurs during the conversion of sce to flow set during the CATALYST::sce2fcs running. Is it possible to add some option to specify truncate_max_range = FALSE within the CATALYST::sce2fcs?

Thanks again for your help.