where to get the gene score for GO analysis in topGO

Question

[liyong]

Hello all,

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.

Answer 1

[liyong]

I figured it out based on one example from the manual.

InterestingGenes = read.delim("interestedGenes.txt", header = FALSE);

tmp = read.delim("TAIR10_representative_gene_models");

geneList = factor(as.integer(tmp$names %in% InterestingGenes));

names(geneList) = tmp$names

then I re-run the previous code, it looks all good.