Question: newSCESet(countData=all.counts) function not working
gravatar for bk11
8 months ago by
bk110 wrote:

Hi I am running through this tutorial But I got this error. I m new to single cell experiment. Why newSCESet(countData=all.counts) function not working? I will appreciate your help. Thanks. I have used these codes:

gunzip("GSE61533_HTSEQ_count_results.xls.gz", remove=FALSE, overwrite=TRUE)
all.counts <- read.xls(’GSE61533_HTSEQ_count_results.xls’, sheet=1, header=TRUE, row.names=1)
sce <- newSCESet(countData=all.counts)

It gave me error:

Error in newSCESet(countData = all.counts) : 
  could not find function "newSCESet"


R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] simpleSingleCell_1.4.1                 TENxBrainData_1.2.0                    HDF5Array_1.10.1                      
 [4] rhdf5_2.26.2                           BiocNeighbors_1.0.0                    BiocFileCache_1.6.0                   
 [7] dbplyr_1.3.0                           DropletUtils_1.2.2                     scRNAseq_1.8.0                        
[10] TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0 GenomicFeatures_1.34.1                 edgeR_3.24.3                          
[13] cluster_2.0.7-1                        dynamicTreeCut_1.63-1                  pheatmap_1.0.12                       
[16] limma_3.38.3                           scran_1.10.2                                     
[19] AnnotationDbi_1.44.0                   readxl_1.2.0                           destiny_2.12.0                        
[22] mvoutlier_2.0.9                        sgeostat_1.0-27                        Rtsne_0.15                            
[25] knitr_1.21                             BiocStyle_2.10.0                       scater_1.10.1                         
[28] ggplot2_3.1.0                          SingleCellExperiment_1.4.1             SummarizedExperiment_1.12.0           
[31] DelayedArray_0.8.0                     BiocParallel_1.16.5                    matrixStats_0.54.0                    
[34] Biobase_2.42.0                         GenomicRanges_1.34.0                   GenomeInfoDb_1.18.1                   
[37] IRanges_2.16.0                         S4Vectors_0.20.1                       BiocGenerics_0.28.0                   
[40] gdata_2.18.0                           R.utils_2.7.0                          R.oo_1.22.0                           
[43] R.methodsS3_1.7.1                      updateR_0.1                            magrittr_1.5                          
[46] stringr_1.3.1                          rvest_0.3.2                            xml2_1.2.0                            
[49] dplyr_0.7.8                            usethis_1.4.0                          devtools_2.0.1                        

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1                rtracklayer_1.42.1            ggthemes_4.0.1               
  [4] prabclus_2.2-7                GGally_1.4.0                  bit64_0.9-7                  
  [7] data.table_1.12.0             RCurl_1.95-4.11               callr_3.1.1                  
 [10] RSQLite_2.1.1                 proxy_0.4-22                  bit_1.1-14                   
 [13] httpuv_1.4.5.1                assertthat_0.2.0              viridis_0.5.1                
 [16] xfun_0.4                      hms_0.4.2                     promises_1.0.1               
 [19] evaluate_0.12                 DEoptimR_1.0-8                progress_1.2.0               
 [22] igraph_1.2.2                  DBI_1.0.0                     reshape_0.8.8                
 [25] purrr_0.2.5                   selectr_0.4-1                 backports_1.1.3              
 [28] trimcluster_0.1-2.1           sROC_0.1-2                    biomaRt_2.38.0               
 [31] remotes_2.0.2                 TTR_0.23-4                    abind_1.4-5                  
 [34] RcppEigen_0.           withr_2.1.2                   robustbase_0.93-3            
 [37] vcd_1.4-4                     GenomicAlignments_1.18.1      xts_0.11-2                   
 [40] prettyunits_1.0.2             mclust_5.4.2                  ExperimentHub_1.8.0          
 [43] lazyeval_0.2.1                laeken_0.5.0                  crayon_1.3.4                 
 [46] pkgconfig_2.0.2               zCompositions_1.1.2           vipor_0.4.5                  
 [49] pkgload_1.0.2                 nnet_7.3-12                   bindr_0.1.1                  
 [52] rlang_0.3.1                   diptest_0.75-7                pls_2.7-0                    
 [55] AnnotationHub_2.14.2          cellranger_1.1.0              rprojroot_1.3-2              
 [58] lmtest_0.9-36                 Matrix_1.2-15                 carData_3.0-2                
 [61] Rhdf5lib_1.4.2                boot_1.3-20                   zoo_1.8-4                    
 [64] beeswarm_0.2.3                processx_3.2.1                viridisLite_0.3.0            
 [67] bitops_1.0-6                  Biostrings_2.50.2             blob_1.1.1                   
 [70] DelayedMatrixStats_1.4.0      scales_1.0.0                  memoise_1.1.0                
 [73] plyr_1.8.4                    zlibbioc_1.28.0               compiler_3.5.1               
 [76] RColorBrewer_1.1-2            rrcov_1.4-7                   Rsamtools_1.34.0             
 [79] cli_1.0.1                     XVector_0.22.0                ps_1.3.0                     
 [82] MASS_7.3-51.1                 tidyselect_0.2.5              stringi_1.2.4                
 [85] forcats_0.3.0                 yaml_2.2.0                    locfit_1.5-9.1               
 [88] grid_3.5.1                    tools_3.5.1                   rio_0.5.16                   
 [91] rstudioapi_0.9.0              foreign_0.8-71                gridExtra_2.3                
 [94] smoother_1.1                  scatterplot3d_0.3-41          digest_0.6.18                
 [97] BiocManager_1.30.4            shiny_1.2.0                   fpc_2.1-11.1                 
[100] bindrcpp_0.2.2                Rcpp_1.0.0                    car_3.0-2                    
[103] later_0.7.5                   httr_1.4.0                    kernlab_0.9-27               
[106] colorspace_1.4-0              XML_3.98-1.16                 fs_1.2.6                     
[109] truncnorm_1.0-8               splines_3.5.1                 statmod_1.4.30               
[112] sp_1.3-1                      flexmix_2.3-14                sessioninfo_1.1.1            
[115] xtable_1.8-3                  modeltools_0.2-22             R6_2.3.0                     
[118] NADA_1.6-1                    mime_0.6                      pillar_1.3.1                 
[121] htmltools_0.3.6               glue_1.3.0                    VIM_4.7.0                    
[124] cvTools_0.3.2                 class_7.3-15                  interactiveDisplayBase_1.20.0
[127] pkgbuild_1.0.2                pcaPP_1.9-73                  mvtnorm_1.0-8                
[130] lattice_0.20-38               tibble_2.0.1                  curl_3.3                     
[133] ggbeeswarm_0.6.0              gtools_3.8.1                  zip_1.0.0                    
[136] openxlsx_4.1.0                survival_2.43-3               rmarkdown_1.11               
[139] desc_1.2.0                    munsell_0.5.0                 e1071_1.7-0.1                
[142] GenomeInfoDbData_1.2.0        haven_2.0.0                   reshape2_1.4.3               
[145] gtable_0.2.0                  robCompositions_2.0.9
ADD COMMENTlink modified 8 months ago by Aaron Lun25k • written 8 months ago by bk110
Answer: newSCESet(countData=all.counts) function not working
gravatar for Aaron Lun
8 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

Please read the latest version of the workflow at

ADD COMMENTlink written 8 months ago by Aaron Lun25k

I have tried this workflow and still getting the same error

Error in newSCESet(countData = all.counts) : 
  could not find function "newSCESet"
ADD REPLYlink written 8 months ago by bk110

You must be following along with an older version of the workflow than the current one (which Aaron linked to). As far as I know, the newSCEset stuff has been completely replaced by using SingleCellExperiment objects.

You should make sure that you are reading the "release" version of these workflows, as well as the current (release) version of the Bioconductor ecosystem (v3.8) -- which you can check using the following R code packageVersion("BiocVersion")[,1:2].


I see from you sessionInfo that you are using the release versions of bioc software -- so I'm guessing you are just looking at outdated code somewhere ... again, you should be using the relase version of the simpleSingleCell worfklow (if that's the code you are following along with).

ADD REPLYlink modified 8 months ago • written 8 months ago by Steve Lianoglou12k
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