issue with Ensembl

Question

[Maryam]

Hi there,

I am trying to get the gene name using this code

libreNameEnsembl <- as.matrix(cds@rowRanges@elementMetadata@listData$gene_short_name)
GeneNameSymbol <- AnnotationDbi::select(org.Mm.eg.db, keys=GeneNameEnsembl, columns='SYMBOL', keytype='ENSEMBL')

but I keep getting this error:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  object 'GeneNameEnsembl' not found

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] stats4    stats     graphics  grDevices
[5] utils     datasets  methods   base     

other attached packages:
 [1] Hmisc_4.7-2                
 [2] Formula_1.2-4              
 [3] survival_3.4-0             
 [4] lattice_0.20-45            
 [5] org.Mm.eg.db_3.16.0        
 [6] AnnotationDbi_1.60.0       
 [7] Matrix_1.5-3               
 [8] reticulate_1.26            
 [9] dplyr_1.0.10               
[10] magrittr_2.0.3             
[11] ggplot2_3.4.0              
[12] monocle3_1.3.1             
[13] SingleCellExperiment_1.20.0
[14] SummarizedExperiment_1.28.0
[15] GenomicRanges_1.50.2       
[16] GenomeInfoDb_1.34.6        
[17] IRanges_2.32.0             
[18] S4Vectors_0.36.1           
[19] MatrixGenerics_1.10.0      
[20] matrixStats_0.63.0         
[21] Biobase_2.58.0             
[22] BiocGenerics_0.44.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-161           bitops_1.0-7          
 [3] bit64_4.0.5            RColorBrewer_1.1-3    
 [5] httr_1.4.4             backports_1.4.1       
 [7] tools_4.2.2            utf8_1.2.2            
 [9] R6_2.5.1               rpart_4.1.19          
[11] DBI_1.1.3              colorspace_2.0-3      
[13] nnet_7.3-18            withr_2.5.0           
[15] tidyselect_1.2.0       gridExtra_2.3         
[17] bit_4.0.5              compiler_4.2.2        
[19] cli_3.5.0              htmlTable_2.4.1       
[21] DelayedArray_0.24.0    scales_1.2.1          
[23] checkmate_2.1.0        stringr_1.5.0         
[25] digest_0.6.31          foreign_0.8-84        
[27] minqa_1.2.5            XVector_0.38.0        
[29] htmltools_0.5.4        base64enc_0.1-3       
[31] jpeg_0.1-10            pkgconfig_2.0.3       
[33] parallelly_1.33.0      lme4_1.1-31           
[35] fastmap_1.1.0          htmlwidgets_1.6.0     
[37] rlang_1.0.6            rstudioapi_0.14       
[39] RSQLite_2.2.20         generics_0.1.3        
[41] jsonlite_1.8.4         RCurl_1.98-1.9        
[43] GenomeInfoDbData_1.2.9 interp_1.1-3          
[45] Rcpp_1.0.9             munsell_0.5.0         
[47] fansi_1.0.3            lifecycle_1.0.3       
[49] terra_1.6-47           stringi_1.7.8         
[51] MASS_7.3-58.1          zlibbioc_1.44.0       
[53] plyr_1.8.8             grid_4.2.2            
[55] blob_1.2.3             parallel_4.2.2        
[57] listenv_0.9.0          crayon_1.5.2          
[59] deldir_1.0-6           Biostrings_2.66.0     
[61] splines_4.2.2          KEGGREST_1.38.0       
[63] knitr_1.41             pillar_1.8.1          
[65] igraph_1.3.5           boot_1.3-28.1         
[67] codetools_0.2-18       glue_1.6.2            
[69] latticeExtra_0.6-30    data.table_1.14.6     
[71] png_0.1-8              vctrs_0.5.1           
[73] nloptr_2.0.3           gtable_0.3.1          
[75] future_1.30.0          assertthat_0.2.1      
[77] cachem_1.0.6           xfun_0.36             
[79] tibble_3.1.8           memoise_2.0.1         
[81] cluster_2.1.4          globals_0.16.2

Answer 1

[Ram]

Try keys = "GeneNameEnsembl". Quoting something should be your second thought when you see the object not found error. The first would be to make sure you don't expect the object to exist as an object.