Low yield mapping ensembl transcript ids to entrez gene ids in biomart
0
0
Entering edit mode
serpalma.v ▴ 60
@serpalmav-8912
Last seen 2.8 years ago
Germany

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?

 

Thanks

biomart ensembl ensemble mart entrez gene identifiers • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 614 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6