Question: newSCESet(countData=all.counts) function not working
0
gravatar for bk11
12 weeks ago by
bk110
bk110 wrote:

Hi I am running through this tutorial https://f1000research.com/articles/5-2122/v1. 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:

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

It gave me error:

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


sessionInfo()

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

locale:
[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                           org.Mm.eg.db_3.7.0                    
[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_0.3.3.5.0           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 12 weeks ago by Aaron Lun23k • written 12 weeks ago by bk110
Answer: newSCESet(countData=all.counts) function not working
0
gravatar for Aaron Lun
12 weeks ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

Please read the latest version of the workflow at https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html.

ADD COMMENTlink written 12 weeks ago by Aaron Lun23k

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 12 weeks ago by bk110
2

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].

(edit)

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 12 weeks ago • written 12 weeks ago by Steve Lianoglou12k
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