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HelenaLC / CATALYST

Cytometry dATa anALYsis Tools
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Error in validObject(result) : invalid class “SingleCellExperiment” object: no 'colPairs' field in 'int_colData' #125

Closed france-hub closed 4 years ago

france-hub commented 4 years ago

Hi Helena,

Thank you for the wonderful package and your workflow. I apologize for the naive question.

I am trying to analyse some mass cytometry data but I am running into the following error when I use the prepData function: sce_ <- prepData(fs, panel, md) Errorin validObject(result) : invalid class “SingleCellExperiment” object: no 'colPairs' field in ``'int_colData'

I've used your package with other data and I've never encountered this type of error. Could you help me to understand what type of error is it?

Thank you again

Francesco

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base

other attached packages: [1] readxl_1.3.1 destiny_3.3.0
[3] knn.covertree_1.0 slingshot_1.7.3
[5] princurve_2.1.4 ggrepel_0.8.2
[7] reshape2_1.4.4 ggcyto_1.17.0
[9] flowWorkspace_4.1.1 ncdfFlow_2.35.0
[11] BH_1.72.0-3 RcppArmadillo_0.9.900.2.0
[13] scater_1.17.2 scran_1.17.2
[15] stringr_1.4.0 diffcyt_1.9.7
[17] CATALYST_1.13.1 SingleCellExperiment_1.11.6 [19] SummarizedExperiment_1.19.6 DelayedArray_0.15.7
[21] matrixStats_0.56.0 Biobase_2.49.0
[23] GenomicRanges_1.41.5 GenomeInfoDb_1.25.8
[25] IRanges_2.23.10 S4Vectors_0.27.12
[27] BiocGenerics_0.35.2 uwot_0.1.8
[29] Matrix_1.2-18 RColorBrewer_1.1-2
[31] ggthemes_4.2.0 dplyr_1.0.0
[33] Rtsne_0.15 cluster_2.1.0
[35] FlowSOM_1.21.0 igraph_1.2.5
[37] cytofkit2_2.0.1 plyr_1.8.6
[39] ggplot2_3.3.2 cytofCore_0.4
[41] rstudioapi_0.11 flowCore_2.1.1

loaded via a namespace (and not attached): [1] reticulate_1.15 lme4_1.1-23
[3] tidyselect_1.1.0 htmlwidgets_1.5.1
[5] BiocParallel_1.23.2 grid_4.0.0
[7] ranger_0.12.1 munsell_0.5.0
[9] codetools_0.2-16 statmod_1.4.34
[11] miniUI_0.1.1.1 withr_2.2.0
[13] colorspace_1.4-1 robustbase_0.93-6
[15] vcd_1.4-7 VIM_6.0.0
[17] TTR_0.23-6 GenomeInfoDbData_1.2.3
[19] vctrs_0.3.2 generics_0.0.2
[21] TH.data_1.0-10 R6_2.4.1
[23] doParallel_1.0.15 ggbeeswarm_0.6.0
[25] clue_0.3-57 rsvd_1.0.3
[27] pdist_1.2 RcppEigen_0.3.3.7.0
[29] VGAM_1.1-3 locfit_1.5-9.4
[31] bitops_1.0-6 promises_1.1.1
[33] scales_1.1.1 multcomp_1.4-13
[35] nnet_7.3-14 beeswarm_0.2.3
[37] gtable_0.3.0 RProtoBufLib_2.1.0
[39] sandwich_2.5-1 rlang_0.4.7
[41] scatterplot3d_0.3-41 GlobalOptions_0.1.2
[43] splines_4.0.0 hexbin_1.28.1
[45] yaml_2.2.1 abind_1.4-5
[47] httpuv_1.5.4 RBGL_1.65.0
[49] tools_4.0.0 ellipsis_0.3.1
[51] gplots_3.0.4 proxy_0.4-24
[53] ggridges_0.5.2 Rcpp_1.0.4.6
[55] base64enc_0.1-3 zlibbioc_1.35.0
[57] purrr_0.3.4 RCurl_1.98-1.2
[59] viridis_0.5.1 GetoptLong_1.0.2
[61] cowplot_1.0.0 zoo_1.8-8
[63] haven_2.3.1 fs_1.4.2
[65] magrittr_1.5 data.table_1.12.8
[67] RSpectra_0.16-0 openxlsx_4.1.5
[69] circlize_0.4.10 colourpicker_1.0
[71] lmtest_0.9-37 RANN_2.6.1
[73] pcaMethods_1.81.0 mvtnorm_1.1-1
[75] hms_0.5.3 mime_0.9
[77] xtable_1.8-4 smoother_1.1
[79] XML_3.99-0.4 rio_0.5.16
[81] jpeg_0.1-8.1 gridExtra_2.3
[83] shape_1.4.4 compiler_4.0.0
[85] tibble_3.0.3 KernSmooth_2.23-17
[87] crayon_1.3.4 minqa_1.2.4
[89] htmltools_0.5.0 mgcv_1.8-31
[91] later_1.1.0.1 tidyr_1.1.0
[93] RcppParallel_5.0.2 ComplexHeatmap_2.5.3
[95] MASS_7.3-51.6 rappdirs_0.3.1
[97] boot_1.3-25 car_3.0-8
[99] permute_0.9-5 gdata_2.18.0
[101] forcats_0.5.0 pkgconfig_2.0.3
[103] foreign_0.8-80 laeken_0.5.1
[105] sp_1.4-2 scuttle_0.99.11
[107] foreach_1.5.0 vipor_0.4.5
[109] dqrng_0.2.1 XVector_0.29.3
[111] drc_3.0-1 digest_0.6.25
[113] tsne_0.1-3 ConsensusClusterPlus_1.53.0 [115] vegan_2.5-6 graph_1.67.1
[117] cellranger_1.1.0 edgeR_3.31.4
[119] DelayedMatrixStats_1.11.1 curl_4.3
[121] shiny_1.5.0 gtools_3.8.2
[123] ggplot.multistats_1.0.0 nloptr_1.2.2.2
[125] rjson_0.2.20 lifecycle_0.2.0
[127] nlme_3.1-148 jsonlite_1.6.1
[129] BiocNeighbors_1.7.0 carData_3.0-4
[131] limma_3.45.9 viridisLite_0.3.0
[133] pillar_1.4.6 lattice_0.20-41
[135] shinyFiles_0.8.0 fastmap_1.0.1
[137] plotrix_3.7-8 DEoptimR_1.0-8
[139] survival_3.2-3 glue_1.4.1
[141] xts_0.12-0 zip_2.0.4
[143] png_0.1-7 iterators_1.0.12
[145] Rgraphviz_2.33.0 class_7.3-17
[147] stringi_1.4.6 nnls_1.4
[149] RcppHNSW_0.2.0 BiocSingular_1.5.0
[151] CytoML_2.1.0 latticeExtra_0.6-29
[153] caTools_1.18.0 cytolib_2.1.2
[155] ape_5.4 irlba_2.3.3
[157] e1071_1.7-3

HelenaLC commented 4 years ago

I have not seen this error before as well, nor have I ever heard of colPairs- I noticed that your SingleCellExperiment version is 1.11.x, mine is 1.10.x. Is it possible this is the development version? Similarlyy, CATALYST is 1.13.x, which is the development version; the release should be 1.12.x... Could you check what your BiocManager::version() is? For the stable release, it should be 3.11.

france-hub commented 4 years ago

Great!! I've run BiocManager::install(version="3.11") and it worked!

Thank you for your quick and helpful answer.

Francesco

Biomiha commented 3 years ago

Hi Helena,

I'm experiencing this error as well even though my Bioconductor version is 3.11. The offending function seems to be:

int_colData(sce) <- icd

I replaced the call instead with the standard setter function: 

colData(sce) <- as(cbind(colData(sce), icd), Class = "DataFrame")

And that did the trick for me.

Thanks.