Question: empty go terms with bioMart
gravatar for chawla
8.5 years ago by
chawla190 wrote:
Hi I am trying to find GO terms (go biological process Ids) for a set of 2195 unique "affy_hg_u133a_2" probe ids. >goterms=getBM(attributes = c("affy_hg_u133a_2", "go_biological_process_id","entrezgene"), filters = "affy_hg_u133a_2", values = data[,1], mart = ensembl) > head(goterms) affy_hg_u133a_2 go_biological_process_id entrezgene 1 209891_at GO:0051301 57405 2 209891_at GO:0007052 57405 3 209891_at GO:0007059 57405 4 209891_at GO:0007049 57405 5 209891_at GO:0007067 57405 6 206204_at GO:0007165 2888 > dim(goterms) [1] 15088 3 > length(unique(goterms[,1])) [1] 1875 > length(which(goterms[,2]=="")) [1] 1222 My question is if out of 2195 unique probe ids, 1875 genes have the go terms for biological process id and are present in the result, but then why 1222 rows have "" as biological process id. They should simply be absent from the result, is something wrong ? if not I will have to filter them each time I use Biomart for Go terms extraction. The same problem occurred with yeast and rat data. Thanks in advance Konika
go yeast probe process biomart • 783 views
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