Hi Remo,

This is related to the previously reported errors, resulting in

 Error in `[.data.frame`(result, , attributes) :
  undefined columns selected

I've fixed this in biomaRt 2.17.1 which should become available for
download soon.
For you current biomaRt version to work, just set bmHeader=FALSE in your
getBM query and things should work:

ipa =
getBM(attributes=c('ensembl_gene_id','mmusculus_inter_paralog_ensembl_gene'),mart=mart,bmHeader=FALSE)

Cheers,
Steffen



On Thu, May 23, 2013 at 1:32 PM, Remo Sanges <noncoding@gmail.com> wrote:

> Dear BioConducters,
>
> I am experiencing errors from the biomaRt package when I try to get
> inter_paralog_ensembl_gene. The strange error I get is the following:
>
> Error in `[.data.frame`(result, , attributes) :
>   undefined columns selected
>
> It happens when I use the ensembl mart asking for all the attributes
> involving xxxxx_inter_paralog_ensembl_**gene even if they are correctly
> listed when I ask for listAttributes(). The behaviour is the same if I use
> the very last version biomart at ensembl setting host="ensembl.org".
>
> Am I doing something wrong?
>
> Here is a sample code of which the last line reproduces the error:
>
> library('biomaRt')
> db = 'hsapiens_gene_ensembl'
> mart = useMart('ensembl',dataset=db)
> hom = getBM(attributes=c('ensembl_**gene_id','mmusculus_homolog_**
> ensembl_gene'),mart=mart)
> ipa = getBM(attributes=c('ensembl_**gene_id','mmusculus_inter_**
> paralog_ensembl_gene'),mart=**mart)
>
> Here are my session info:
>
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.16.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-4.1 tools_3.0.0    XML_3.95-0.2
>
> Many Thanks
>
> Kind Regards
>
> ERemo
>
> --
> Remo Sanges - Ph.D.
> Bioinformatics - Animal Physiology and Evolution
> Stazione Zoologica Anton Dohrn
> Villa Comunale, 80121 Napoli - Italy
> +39 081 5833428
>
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