Question: Missing Gene Symbols From Mgi With Biomart (Mouse)
0
gravatar for traversc
5.2 years ago by
traversc0
traversc0 wrote:

I'm trying to use biomaRt to get attributes for a bunch of genes. When I try it, I notice that there are some missing values. Can someone tell me why?

Ex.:

library(biomaRt) mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")

results <- getBM(attributes = c("gene_biotype", "mgi_symbol"), filters = "mgi_symbol", values = "Gm4890", mart = mart)

Yet I can see the gene plainly hhere: http://www.informatics.jax.org/marker/MGI:3779445

R biomart mouse • 3.1k views
ADD COMMENTlink modified 5.2 years ago by Emily_Ensembl18k • written 5.2 years ago by traversc0
0
gravatar for Emily_Ensembl
5.2 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

I just did your query and got a result:

lincRNA Gm4890

How many IDs did you use in your query? Are you using the latest version (74), because the name Gm4890 wasn't assigned in previous databases?

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Emily_Ensembl18k

How do I check which version of ensembl I am using with biomaRt? I assumed it would use the latest, since it pulls from the online database?

I don't think that is the issue anyway, because these IDs came from fairly old reference files.

ADD REPLYlink written 5.2 years ago by traversc0

It definitely works with the current database, because I tried it.

How many IDs did you use in your query?

ADD REPLYlink written 5.2 years ago by Emily_Ensembl18k

Thank you Emily.

I figured out the problem in case anyone was wondering... I just needed to update Bioconductor

/slaps forehead

ADD REPLYlink written 5.2 years ago by traversc0
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