Hello,

I am trying to run a GO analysis on a set of genes I identified, but I am getting an error. Does anyone have any ideas? Thank you so much in advance!

library(org.Mm.eg.db)
library(topGO)

gene_interest <- c("Gm28038"       ,          "Gm14471"          ,       "A730071L15Rik"      ,     "Ap3b1"   ,               
 "Rims2"                  , "Ilf2"        ,            "Mcrip1"     ,             "Gm18821" ,               
 "Manbal"                 , "Cfap20dc",                "Snhg8"    ,               "Mir6951",                
 "Aurkb"                  , "Mroh8"     ,              "Cog4"       ,             "Tmeff1"    ,             
 "Gm38393"                , "Gm6733"    ,              "Fbxl13"   ,               "Gm8539"  ,               
 "Gm17484"                , "Prim2"     ,              "Zfp518a"  ,               "Golga1"  ,               
 "Acaa2"                  , "Zfp609"    ,              "Nup188"   ,               "Gm4673"  ,               
 "Rpl23a"                 , "Mfsd10"    ,              "Gm15614"  ,               "ENSMUSG00000121395" ,     
 "Tmem181b-ps"            , "Spint1"    ,              "Cdv3"       ,             "Gm21063" ,               
 "Timm22"                 , "Atg4b"     ,              "Ska2"       ,             "Lsr"         ,           
  "Mrps28"    ,              "Edc3"       ,             "Gm6643"    ,             
 "Supt20"                 , "Hmgn3"     ,              "Xlr5a"      ,             "Picalm"    ,             
 "Gm12097"                , "Aimp1"     ,              "Sf3b3"      ,             "Map1b"  )

annotations <- select(org.Mm.eg.db, keys = gene_interest, keytype = "SYMBOL", columns = "GO")

GOdata <- new(
  "topGOdata",
  ontology = "BP",  # Specify the GO ontology ("BP" for Biological Process, "MF" for Molecular Function, "CC" for Cellular Component)
  allGenes = gene_interest,
  nodeSize = 10,  # The minimum number of genes in a GO term
  annot = annotations
)

################################### ERROR

Error in .local(.Object, ...) : allGenes must be a named vector

sessionInfo( )

R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: Europe/Rome
tzcode source: internal

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

other attached packages:
 [1] topGO_2.52.0                SparseM_1.81                GO.db_3.17.0               
 [4] graph_1.78.0                org.Mm.eg.db_3.17.0         AnnotationDbi_1.63.2       
 [7] BiocManager_1.30.21.1       SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
[10] Biobase_2.60.0              GenomicRanges_1.52.0        GenomeInfoDb_1.36.1        
[13] IRanges_2.34.1              S4Vectors_0.38.1            BiocGenerics_0.46.0        
[16] MatrixGenerics_1.12.2       matrixStats_1.0.0          

loaded via a namespace (and not attached):
 [1] KEGGREST_1.40.0         gtable_0.3.3            xfun_0.39               ggplot2_3.4.2          
 [5] htmlwidgets_1.6.2       lattice_0.21-8          vctrs_0.6.3             tools_4.3.0            
 [9] bitops_1.0-7            generics_0.1.3          parallel_4.3.0          tibble_3.2.1           
[13] fansi_1.0.4             RSQLite_2.3.1           blob_1.2.4              pkgconfig_2.0.3        
[17] Matrix_1.6-0            data.table_1.14.8       dbplyr_2.3.3            lifecycle_1.0.3        
[21] GenomeInfoDbData_1.2.10 compiler_4.3.0          Biostrings_2.68.1       munsell_0.5.0          
[25] DESeq2_1.40.2           codetools_0.2-19        htmltools_0.5.5         RCurl_1.98-1.12        
[29] pillar_1.9.0            crayon_1.5.2            BiocParallel_1.34.2     cachem_1.0.8           
[33] DelayedArray_0.26.6     tidyselect_1.2.0        locfit_1.5-9.8          digest_0.6.33          
[37] dplyr_1.1.2             fastmap_1.1.1           grid_4.3.0              colorspace_2.1-0       
[41] cli_3.6.1               magrittr_2.0.3          S4Arrays_1.0.4          utf8_1.2.3             
[45] scales_1.2.1            bit64_4.0.5             httr_1.4.6              XVector_0.40.0         
[49] bit_4.0.5               png_0.1-8               memoise_2.0.1           knitr_1.43             
[53] rlang_1.1.1             Rcpp_1.0.11             glue_1.6.2              DBI_1.1.3              
[57] rstudioapi_0.15.0       R6_2.5.1                zlibbioc_1.46.0

According to topGO documentation : "The geneList data [...] contains just a small number of genes with the corespondent p-values. ". It should be a name vector which identifiers as names and p-values as values.