Question: Low yield mapping ensembl transcript ids to entrez gene ids in biomart
gravatar for serpalma.v
3.8 years ago by
serpalma.v60 wrote:

Hello everyone,

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?



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