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mtrussart / CytofRUV

CytofRUV: Removing unwanted variation to integrate multiple CyTOF datasets.
https://mtrussart.github.io/CytofRUV/
GNU General Public License v3.0
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Error in load_data #31

Closed northern-soul-marie91 closed 2 years ago

northern-soul-marie91 commented 2 years ago

Hi Marie,

I'm getting the following error when I run

data=load_data(wd_data,metadata_filename,panel_filename)

[1] "Formatting Data" Error in levels<-(*tmp*, value = as.character(levels)) : factor level [2] is duplicated

I can't work out what this is an error in.

session info

Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] shinycssloaders_1.0.0       ComplexHeatmap_2.8.0       
 [3] writexl_1.4.0               shinydashboard_0.7.1       
 [5] shinyjs_2.0.0               shiny_1.6.0                
 [7] ConsensusClusterPlus_1.56.0 FlowSOM_2.0.0              
 [9] igraph_1.2.6                purrr_0.3.4                
[11] ruv_0.9.7.1                 readxl_1.3.1               
[13] ggplot2_3.3.5               CytofRUV_0.1               
[15] CATALYST_1.16.0             Seurat_4.0.3               
[17] SeuratObject_4.0.2          SingleCellExperiment_1.14.1
[19] SummarizedExperiment_1.22.0 Biobase_2.52.0             
[21] GenomicRanges_1.44.0        GenomeInfoDb_1.28.0        
[23] IRanges_2.26.0              S4Vectors_0.30.0           
[25] BiocGenerics_0.38.0         MatrixGenerics_1.4.0       
[27] matrixStats_0.59.0          flowCore_2.4.0             

loaded via a namespace (and not attached):
  [1] scattermore_0.7           flowWorkspace_4.4.0       tidyr_1.1.3              
  [4] irlba_2.3.3               multcomp_1.4-17           DelayedArray_0.18.0      
  [7] data.table_1.14.0         rpart_4.1-15              RCurl_1.98-1.3           
 [10] doParallel_1.0.16         generics_0.1.0            ScaledMatrix_1.0.0       
 [13] cowplot_1.1.1             TH.data_1.0-10            RANN_2.6.1               
 [16] future_1.21.0             ggpointdensity_0.1.0      spatstat.data_2.1-0      
 [19] xml2_1.3.2                httpuv_1.6.1              assertthat_0.2.1         
 [22] viridis_0.6.1             hms_1.1.0                 promises_1.2.0.1         
 [25] fansi_0.5.0               Rgraphviz_2.36.0          DBI_1.1.1                
 [28] htmlwidgets_1.5.3         spatstat.geom_2.2-0       ellipsis_0.3.2           
 [31] dplyr_1.0.7               ggcyto_1.20.0             ggnewscale_0.4.5         
 [34] ggpubr_0.4.0              backports_1.2.1           cytolib_2.4.0            
 [37] RcppParallel_5.1.4        deldir_0.2-10             sparseMatrixStats_1.4.0  
 [40] vctrs_0.3.8               Cairo_1.5-12.2            ROCR_1.0-11              
 [43] abind_1.4-5               withr_2.4.2               ggforce_0.3.3            
 [46] aws.signature_0.6.0       sctransform_0.3.2         goftest_1.2-2            
 [49] cluster_2.1.2             lazyeval_0.2.2            crayon_1.4.1             
 [52] drc_3.0-1                 pkgconfig_2.0.3           tweenr_1.0.2             
 [55] nlme_3.1-152              vipor_0.4.5               rlang_0.4.11             
 [58] globals_0.14.0            lifecycle_1.0.0           miniUI_0.1.1.1           
 [61] sandwich_3.0-1            rsvd_1.0.5                cellranger_1.1.0         
 [64] polyclip_1.10-0           lmtest_0.9-38             graph_1.70.0             
 [67] Matrix_1.3-4              carData_3.0-4             zoo_1.8-9                
 [70] base64enc_0.1-3           beeswarm_0.4.0            ggridges_0.5.3           
 [73] GlobalOptions_0.1.2       pheatmap_1.0.12           png_0.1-7                
 [76] viridisLite_0.4.0         rjson_0.2.20              bitops_1.0-7             
 [79] KernSmooth_2.23-20        DelayedMatrixStats_1.14.0 shape_1.4.6              
 [82] stringr_1.4.0             parallelly_1.26.0         jpeg_0.1-8.1             
 [85] rstatix_0.7.0             ggsignif_0.6.2            aws.s3_0.3.21            
 [88] beachmat_2.8.0            scales_1.1.1              magrittr_2.0.1           
 [91] plyr_1.8.6                hexbin_1.28.2             ica_1.0-2                
 [94] zlibbioc_1.38.0           compiler_4.1.0            RColorBrewer_1.1-2       
 [97] plotrix_3.8-1             clue_0.3-59               fitdistrplus_1.1-5       
[100] XVector_0.32.0            listenv_0.8.0             patchwork_1.1.1          
[103] ncdfFlow_2.38.0           pbapply_1.4-3             MASS_7.3-54              
[106] mgcv_1.8-36               tidyselect_1.1.1          stringi_1.6.2            
[109] forcats_0.5.1             RProtoBufLib_2.4.0        yaml_2.2.1               
[112] BiocSingular_1.8.1        latticeExtra_0.6-29       ggrepel_0.9.1            
[115] tools_4.1.0               future.apply_1.7.0        rio_0.5.27               
[118] CytoML_2.4.0              circlize_0.4.13           rstudioapi_0.13          
[121] foreach_1.5.1             foreign_0.8-81            gridExtra_2.3            
[124] farver_2.1.0              Rtsne_0.15                digest_0.6.27            
[127] Rcpp_1.0.6                car_3.0-11                broom_0.7.8              
[130] scuttle_1.2.0             later_1.2.0               RcppAnnoy_0.0.18         
[133] httr_1.4.2                colorspace_2.0-2          XML_3.99-0.6             
[136] tensor_1.5                reticulate_1.20           splines_4.1.0            
[139] uwot_0.1.10               RBGL_1.68.0               spatstat.utils_2.2-0     
[142] scater_1.20.1             plotly_4.9.4.1            xtable_1.8-4             
[145] jsonlite_1.7.2            R6_2.5.0                  pillar_1.6.1             
[148] htmltools_0.5.1.1         mime_0.11                 nnls_1.4                 
[151] glue_1.4.2                fastmap_1.1.0             BiocParallel_1.26.0      
[154] BiocNeighbors_1.10.0      codetools_0.2-18          mvtnorm_1.1-2            
[157] utf8_1.2.1                lattice_0.20-44           spatstat.sparse_2.0-0    
[160] tibble_3.1.2              curl_4.3.2                ggbeeswarm_0.6.0         
[163] leiden_0.3.8              colorRamps_2.3            gtools_3.9.2             
[166] zip_2.2.0                 openxlsx_4.2.4            survival_3.2-11          
[169] munsell_0.5.0             GetoptLong_1.0.5          GenomeInfoDbData_1.2.6   
[172] iterators_1.0.13          haven_2.4.1               reshape2_1.4.4           
[175] gtable_0.3.0              spatstat.core_2.2-0

I've attached my panel file and metadata Lym_panel.xlsx metadata.xlsx

Best wishes, Marie

northern-soul-marie91 commented 2 years ago

I have now solved this issue. I realised that the sample_id column in metadata should not have duplicate values.