I am working with a non-model organism. So I constructed TERM2GENE and TERM2NAME files and used enricher to run GO enrichment analysis. The code I used was below. Finally, I got 71 GO terms in the result. But actually, there are 99 unique GO terms for my input genes and I have checked that all 99 GO terms exist now, no obsolete ones. I don't know why there are some GO terms missed such as GO:0003700. I checked there are 57 genes having GO:0003700 in my input gene file.
And I set pvaluecutoff and qvaluecutoff = 1 trying to get all results. But I found the outputted genes is less than 356 (#input genes). I was really very confused. I would really appreciate if anyone could give me some suggestions.
result1.0_MF = as.data.frame(enricher(gene=target1.0$GeneID, TERM2GENE=go2gene_MF, TERM2NAME=go2term_MF, pvalueCutoff = 1, qvalueCutoff=1, pAdjustMethod = "fdr"))