[BioC] Follow-up -> ERROR: caught BioMart::Exception:

[Heidi Dvinge]

Hello Maude,

have a look at the attributePages() function. That will tell you what  
kind of attributes are available for the mart connection you're  
using. In combination with listAttributes(..., page=), this will tell  
you what queries can be combined.

Best
\Heidi

On 14 May 2010, at 14:15, <mauede at alice.it> <mauede at alice.it> wrote:

> I tried splitting my initial query into two smaller ones taht are  
> connected by a common attribute which is needed to recombine the  
> information pieces together.
> I realized some combinations work fine whereas I get the same error  
> in other cases:
>
> The following three queirs work
>> genes_map1 <- getBM(attributes=c 
>> ("entrezgene","hgnc_symbol","ensembl_gene_id","ensembl_transcript_id" 
>> ),filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart)
>> genes_map2 <- getBM(attributes=c 
>> ("ensembl_transcript_id","3_utr_start","3_utr_end"),
> + filters = "entrezgene", values=genes.ds[,1], mart=hmart)
>> genes_map3 <- getBM(attributes=c 
>> ("ensembl_gene_id","3_utr_start","3_utr_end"),
> + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart)
>
> The following queries generate the same error
>> genes_map4 <- getBM(attributes=c 
>> ("hgnc_symbol","3_utr_start","3_utr_end"),
> + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart)
> Error in getBM(attributes = c("hgnc_symbol", "3_utr_start",  
> "3_utr_end"),  :
>   Query ERROR: caught BioMart::Exception::Usage: Attributes from  
> multiple attribute pages are not allowed
>> genes_map4 <- getBM(attributes=c 
>> ("entrezgene","3_utr_start","3_utr_end"),
> + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart)
> Error in getBM(attributes = c("entrezgene", "3_utr_start",  
> "3_utr_end"),  :
>   Query ERROR: caught BioMart::Exception::Usage: Attributes from  
> multiple attribute pages are not allowed
>
> Is there any description of the attribute pages ?
> Thank you very much,
> Maura
>
>
>
> tutti i telefonini TIM!
>
>
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