Search
Question: Low yield mapping ensembl transcript ids to entrez gene ids in biomart
0
gravatar for serpalma.v
2.2 years ago by
serpalma.v30
Germany
serpalma.v30 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?

 

Thanks

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by serpalma.v30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 141 users visited in the last hour