Closed LenHC closed 6 months ago
HelenaLC
commented
1 year ago Hard to help given the information you provided. Could you perhaps post the output of running traceback() after the error occurs? Also, please enclose code in code blocks (3 back ticks before and after) to make it more legible 🙏
LenHC
commented
1 year ago Hello Helena, thanks for the reply. I just added traceback() information and enclosed the codes!
HelenaLC
commented
1 year ago The code being run up to this point should be something like this ... I'd suggest running through this to figure out the issue. Looks like something might be off with the FCS file identifiers.
fs <- CATALYST:::.read_fs(fcsdir, "common") # internal helper calling 'flowCore::read.flowSet'
ids0 <- md[[md_cols$file]] # should me 'md$correctedFileName'
ids1 <- fsApply(fs, identifier) # what are these?
ids2 <- keyword(fs, "FILENAME") # and these?
if (length(unlist(ids2)) == length(fs))
ids2 <- basename(ids2)
check1 <- all(ids1 %in% ids0) # what is this?
check2 <- all(ids2 %in% ids0) # and this?
ids_use <- which(c(check1, check2))[1]
ids <- list(ids1, ids2)[[ids_use]]
fs <- fs[match(md[[md_cols$file]], ids) # error hereHello Helena, I see... I will try these suggestions and get back to you.
HelenaLC
commented
6 months ago closing due to inactivity.
Hello, I keep getting "Error: Subset out of bounds" when using prepData. Here is my code:
sce <- prepData(fcsdir, panel=panel, md=metadata, transform=FALSE, panel_cols=list(channel="fcs_colname", antigen="antigen"), md_cols=list(file="correctedFileName", id="SampleID", factors=metaatt), FACS = TRUE)Sessioninfo:
> sessionInfo()R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets [7] methods base
other attached packages: [1] CATALYST_1.24.0 SingleCellExperiment_1.22.0 [3] SummarizedExperiment_1.30.2 Biobase_2.60.0
[5] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[7] IRanges_2.34.1 S4Vectors_0.38.1
[9] BiocGenerics_0.46.0 MatrixGenerics_1.12.2
[11] matrixStats_1.0.0 stringr_1.5.0
[13] cowplot_1.1.1 patchwork_1.1.2
[15] dplyr_1.1.2 magrittr_2.0.3
[17] readxl_1.4.2 xlsx_0.6.5
[19] knitr_1.43 uwot_0.1.16
[21] Matrix_1.5-4.1 tidyr_1.3.0
[23] cyCombine_0.2.15 PeacoQC_1.10.0
[25] flowAI_1.30.0 flowVS_1.32.0
[27] flowStats_4.12.0 flowViz_1.64.0
[29] lattice_0.21-8 ggcyto_1.28.0
[31] flowWorkspace_4.12.0 ncdfFlow_2.46.0
[33] BH_1.81.0-1 ggplot2_3.4.2
[35] flowCore_2.12.0
loaded via a namespace (and not attached): [1] bitops_1.0-7 httr_1.4.6
[3] RColorBrewer_1.1-3 doParallel_1.0.17
[5] Rgraphviz_2.44.0 tools_4.3.0
[7] backports_1.4.1 utf8_1.2.3
[9] R6_2.5.1 mgcv_1.8-42
[11] GetoptLong_1.0.5 withr_2.5.0
[13] gridExtra_2.3 cli_3.6.1
[15] textshaping_0.3.6 sandwich_3.0-2
[17] labeling_0.4.2 nnls_1.4
[19] mvtnorm_1.2-2 robustbase_0.99-0
[21] genefilter_1.82.1 ggridges_0.5.4
[23] systemfonts_1.0.4 colorRamps_2.3.1
[25] rrcov_1.7-4 scater_1.28.0
[27] plotrix_3.8-2 limma_3.56.2
[29] RSQLite_2.3.1 generics_0.1.3
[31] shape_1.4.6 gtools_3.9.4
[33] car_3.1-2 interp_1.1-4
[35] RProtoBufLib_2.12.0 ggbeeswarm_0.7.2
[37] fansi_1.0.4 abind_1.4-5
[39] lifecycle_1.0.3 multcomp_1.4-25
[41] edgeR_3.42.4 carData_3.0-5
[43] Rtsne_0.16 grid_4.3.0
[45] blob_1.2.4 crayon_1.5.2
[47] beachmat_2.16.0 annotate_1.78.0
[49] xlsxjars_0.6.1 KEGGREST_1.40.0
[51] pillar_1.9.0 ComplexHeatmap_2.16.0
[53] rjson_0.2.21 fda_6.1.4
[55] corpcor_1.6.10 codetools_0.2-19
[57] glue_1.6.2 kohonen_3.0.12
[59] data.table_1.14.8 vctrs_0.6.3
[61] png_0.1-8 cellranger_1.1.0
[63] gtable_0.3.3 cachem_1.0.8
[65] ks_1.14.0 xfun_0.39
[67] S4Arrays_1.0.4 fds_1.8
[69] pracma_2.4.2 ConsensusClusterPlus_1.64.0 [71] pcaPP_2.0-3 survival_3.5-5
[73] rJava_1.0-6 iterators_1.0.14
[75] cytolib_2.12.0 TH.data_1.1-2
[77] nlme_3.1-162 bit64_4.0.5
[79] RcppAnnoy_0.0.21 irlba_2.3.5.1
[81] vipor_0.4.5 KernSmooth_2.23-21
[83] colorspace_2.1-0 DBI_1.1.3
[85] mnormt_2.1.1 tidyselect_1.2.0
[87] bit_4.0.5 compiler_4.3.0
[89] graph_1.78.0 BiocNeighbors_1.18.0
[91] DelayedArray_0.26.6 scales_1.2.1
[93] DEoptimR_1.0-14 hexbin_1.28.3
[95] digest_0.6.32 rainbow_3.7
[97] rmarkdown_2.23 XVector_0.40.0
[99] htmltools_0.5.5 pkgconfig_2.0.3
[101] jpeg_0.1-10 changepoint_2.2.4
[103] sparseMatrixStats_1.12.2 highr_0.10
[105] fastmap_1.1.1 rlang_1.1.1
[107] GlobalOptions_0.1.2 DelayedMatrixStats_1.22.1
[109] farver_2.1.1 zoo_1.8-12
[111] BiocParallel_1.34.2 mclust_6.0.0
[113] BiocSingular_1.16.0 RCurl_1.98-1.12
[115] scuttle_1.10.1 GenomeInfoDbData_1.2.10
[117] munsell_0.5.0 Rcpp_1.0.10
[119] viridis_0.6.3 ggnewscale_0.4.9
[121] stringi_1.7.12 zlibbioc_1.46.0
[123] MASS_7.3-60 plyr_1.8.8
[125] parallel_4.3.0 ggrepel_0.9.3
[127] deldir_1.0-9 Biostrings_2.68.1
[129] splines_4.3.0 circlize_0.4.15
[131] locfit_1.5-9.8 igraph_1.5.0
[133] ggpubr_0.6.0 ggsignif_0.6.4
[135] ScaledMatrix_1.8.1 reshape2_1.4.4
[137] XML_3.99-0.14 drc_3.0-1
[139] evaluate_0.21 emdist_0.3-2
[141] latticeExtra_0.6-30 deSolve_1.36
[143] foreach_1.5.2 tweenr_2.0.2
[145] purrr_1.0.1 polyclip_1.10-4
[147] clue_0.3-64 ggforce_0.4.1
[149] rsvd_1.0.5 broom_1.0.5
[151] xtable_1.8-4 rstatix_0.7.2
[153] viridisLite_0.4.2 IDPmisc_1.1.20
[155] ragg_1.2.5 tibble_3.2.1
[157] beeswarm_0.4.0 memoise_2.0.1
[159] FlowSOM_2.8.0 AnnotationDbi_1.62.2
[161] cluster_2.1.4 sva_3.48.0
[163] hdrcde_3.4
> head(panel)A tibble: 6 × 2 fcs_colname antigen