I am trying to use topGO in R to do GO analysis for my 140 interested Arabidopsis genes. To define the gene universe, I collect all Arabidopsis genes from (https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_gene_lists/TAIR10_representative_gene_models) to genelist.
when I run
GOdata = new("topGOdata", ontology = "MF", allGenes = genelist, annot = annFUN.org, mapping = "org.At.tair.db"), I got error
"allGenes must be a named vector". In the manual, it says "allGenes needs a list of gene ids and the gene-wise scores".
However, I only have the gene ids, not sure how I could get the corresponding scores. Can anyone point me to the right direction?
Thanks a lot.