It seems biomart.org does not have a working version of the underlying
mart. Since you are using biomaRt, you can connect directly to the original
source of this dataset in the useMart(...) function. Below is an example
call that should work - i think (not tested),
mart <- useMart(
biomart = "bacteria_mart_15",
dataset = "bac_20000_gene",
host = "bacteria.ensembl.org",
path = "/biomart/martservice"
);
HTH
Syed
On 10 September 2012 15:46, Gurudutta Panda <[email protected]>wrote:
> Hii All,
>
> i am facing a problem in which the datasets for certain bacteria are empty.
> Can anyone please suggest what might be going wrong or is it something to
> do with my commands in R(which i have tried to rule out by using the same
> syntax for other datasets).
>
> I am getting the following output.
> """"
> I. For e.coli its fine!
>
> > ecoli<- useMart("bacteria_mart_14",dataset="esc_18_gene")
> > check<-getBM(attribute=c("strand"),mart=ecoli)
> > check
> strand
> 1 -1
> 2 1
>
> II. For B. anthracis Ames ancestor, its giving empty datasets
>
> > gbaa<-useMart("bacteria_mart_14",dataset="bac_20000_gene")
> > check<-getBM(attribute=c("strand"),mart=gbaa)
> > check
> [1] strand
> <0 rows> (or 0-length row.names)
>
> III my session info
>
> > sessionInfo()
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/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_2.8.1 SpeCond_1.6.0 RColorBrewer_1.0-5 hwriter_1.3
> fields_6.6.2 spam_0.27-0
> [7] Biobase_2.12.2 mclust_3.4.11
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.8-0 tools_2.13.2 XML_3.6-2
>
>
> Can anyone please help
>
> Regards
> gurudutta
>
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