I have a vector of 2906 ensembl transcript ids and I want to find their entrez gene ids using biomart, so I can do pathway analysis with gage.
The problem is that using the code below, I only obtain 404 out of 2906.
The ensemble transcript ids come from the annotations provided by affymetrix's "PorGene-1_1-st", selecting only probes in the "main" category.
mart <- useMart("ensembl") ds <- useDataset("sscrofa_gene_ensembl", mart) getBM(attributes = c("entrezgene", "ensembl_transcript_id"), filters = "ensembl_transcript_id", values = vals, mart = ds)
Could you help me to find a way to maximize the yield of query?