[BioC] BiomaRt error: ncol(result) == length(attributes) is not TRUE

[Steffen]

Hi Quin,

How long is your list of identifiers?  It is not recommended to run a 
query like this in loops as this causes the web service to go out of 
sync at some point during the loop.
biomaRt is made to perform batch queries.
I would recommend to do your query as follows:

genes <- getGene(id=ID, type="refseq_dna", mart=ensembl)

This will give you a dataframe with the info for all the genes. If 
needed you can then loop over the result.
If you feel like you really need to loop you could add Sys.sleep(1) in  
the loop.

Cheers,
Steffen

Quin Wills wrote:
> Hello all
>
> I'm running the most up to date R and biomaRt.
>
> I get the following error:
>  >Error: ncol(result) == length(attributes) is not TRUE
>
> for the following loop:
> # 'ID' is a character vector of refseq IDs
> #'gene', for the purposes of the argument here, is a list storing the output
>
>  > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
>  > for (i in 1:length(ID)) {
>  >       gene[[i]] <- getGene(id=ID[i], type="refseq_dna", mart=ensembl)
>  > }
>
> The problem is not dependent on the get function used or the id type 
> used. I didn't have this problem yesterday on the same script. The error 
> also occurs randomly, breaking the loop at any particular point, 
> sometimes allowing thousands of loops to run.
>
> Could this be a problem with the server I'm pulling the information 
> from? It just seems too random to be my coding - especially considering 
> I didn't have this problem yesterday.
>
> I've had this before, ages ago, and would like to get to the bottom of 
> it. And wisdom? Thanks.
>  
>
> * *
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> * *
>
> * *
>
> *Quin Wills*
> *DPhil candidate*
>
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>
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>
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>
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>
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-- 
----------------------------------------------------------------
Steffen Durinck, PhD

Division of Biostatistics, University of California, Berkeley &
Life Sciences Department, Lawrence Berkeley National Laboratory
1 cyclotron Rd, Berkeley
CA, 94720, USA
Tel: +1-510-486-5202