[BioC] BioMart Error
Wolfgang Huber
whuber at embl.de
Tue Sep 22 15:46:51 CEST 2009
Hi Lakshmanan
thank you for reporting this and apologies for the delayed reply. It
turns out that there is a disagreement about the format of the data
reported from the SNP biomart webservice that you are querying and the
biomaRt R package.
Resolving this seems to be a complex and slow procedure. For the time
being, please do not use biomaRt with the SNP biomart, it will not work.
Best wishes
Wolfgang
-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
-------------------------------------------------------
> -------- Original Message --------
> Subject: [BioC] BioMart Error
> Date: Fri, 4 Sep 2009 10:54:19 -0400
> From: Lakshmanan Iyer <laxvid at gmail.com>
> To: Bioconductor at stat.math.ethz.ch
>
> Hi,
> I Ran the following code and it did not work and asked me to report the
> error to the list. So here it is:
> ### Code####
> library (biomaRt);
> snps <- useMart("snp", dataset="hsapiens_snp");
> filters <- listFilters(snps);
> attributes <- listAttributes(snps);
> #
> required_attributes <- attributes[,1]
> required_list <- c("ENSG00000006638" ,"ENSG00000110148");
> i22 <- getBM( attributes=required_attributes[30:45],
> filters="ensembl_gene", values=required_list, mart=snps)
> ### Code End ###
>
> and got the following error:
>>>>>>>>>>>>>>
> Error in getBM(attributes = required_attributes[30:45], filters =
> "ensembl_gene", :
> The query to the BioMart webservice returned an invalid result: the
> number
> of columns in the result table does not equal the number of attributes in
> the query. Please report this to the mailing list.
>>>>>>>>>>>>>>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i486-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.97-3 XML_2.3-0
>
> -Best
> -Lax
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
More information about the Bioconductor
mailing list