Dear Jim and all,
    Thank you! I have changed the EntrezGene IDs to ensembl IDs to redo it.
A simple example is as the following:
dnds <- getBM(attributes = c("ensembl_gene_id",
"mmusculus_homolog_dn","mmusculus_homolog_ds"), filters =
"ensembl_gene_id", values = "ENSG00000139618", mart = mart)
But there is an error as the following:
Error in `[.data.frame`(result, , attributes) :
  undefined columns selected

Could you give me some suggestion about this? Thank you very much!

On Tue, Mar 19, 2013 at 12:03 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi David,
>
>
>
> On 3/19/13 12:26 PM, David Wang wrote:
> There are certain attribute pages on the Biomart server, and you cannot
> get data from more than one.
>
> > x <- listAttributes(mart, what=c("name","description","**page"))
> > x[x[,1] %in% c("entrezgene","mmusculus_**homolog_dn","mmusculus_**
> homolog_ds"),]
>                     name   description         page
> 47            entrezgene EntrezGene ID feature_page
> 577 mmusculus_homolog_dn            dN     homologs
> 578 mmusculus_homolog_ds            dS     homologs
>
> So the homolog data you want come from the homologs page, but the
> entrezgene data come from the feature_page, hence you cannot get all three
> at one time.
>
> Best,
>
> Jim
>
>
> --
David Wang

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