so I want to assign GO IDs to a list of genes (I have the genname and entrez). I am using Biomart for this with the following code:
ensembl = useMart("ensembl") ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl) dat <- read.csv("Workbook10.csv", header = FALSE) result1 <- getBM(attributes = c("external_gene_name", "entrezgene", "go_id""), filters = "entrezgene", values = dat, mart = ensembl)
in my workbook I have a list of mouse genes (their entrez codes)
in principle this works and I get for almost all genes their GO IDs assigned, however when I check for some examples, they are missing entirely and those are genes which definitely have GO IDs, I checked it.
Does anyone know what the problem is?
Any help would be highly appreciated!