gravatar for morteza.aslanzadeh

3 hours ago by

I have search a lot of online sources to solve this problem but couldn't. I'm using getBM() function of biomaRt but getting an error. I have used this code like 7 months ago without any error but now it's giving error and I think it should probably be because of the server ????

what I use:

db <- useMart('ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl', host="www.ensembl.org")
go_ids <- getBM(attributes=c('go_id', 'ensembl_gene_id', 'namespace_1003'), filters='ensembl_gene_id', values=bg_genes, mart=db)

values=bg_genes is around ~20000 gene ids. I tried with less gene ids (10) then it worked.

The ERROR:

Error in getBM(attributes = c("go_id", "ensembl_gene_id", "namespace_1003"),  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org

It there any other way to solve this? I need all my ~20000 in values=bg_genes



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