[BioC] Problem retrieving dN/dS from Biomart

[James W. MacDonald]

Hi Marcus,

You don't give sessionInfo(), so no idea if you have an outdated 
version or whatever. But this works for me.

> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> getBM(c("mmusculus_homolog_dn","mmusculus_homolog_ds"), "hgnc_symbol", "GABRA6", mart)
  mmusculus_homolog_dn mmusculus_homolog_ds
1               0.0459               0.5686
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] 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_2.18.0  lattice_0.20-27 statmod_1.4.18  limma_3.18.13

loaded via a namespace (and not attached):
[1] compiler_3.0.2 grid_3.0.2     RCurl_1.95-4.1 tools_3.0.2    
XML_3.98-1.1

Best,

Jim



On Friday, March 14, 2014 1:40:12 PM, Marcus Goldberg wrote:
> I attempted to retrieve values of dn and ds for human/mouse gene
> comparisons in Ensembl using BiomaRt (R application), and get the following
> error (with mart defined as ensembl human reference genome):
>
> t = getBM(attributes = "mmusculus_homolog_dn", filters =
> "hgnc_symbol", values = "GABRA6", mart = mart)
> Error in `[.data.frame`(result, , attributes) :
>   undefined columns selected
>
> In contrast, if I try to retrieve some other attribute, such as mouse gene
> id, it works (e.g.)
>
>> t = getBM(attributes = "mmusculus_homolog_ensembl_gene", filters = "hgnc_symbol", values = "GABRA6", mart = mart)
>> t
>     [1] "ENSMUSG00000020428"
>
> So it doesn't seem to be a syntax error. What am I doing wrong in calling
> the "mmmusculus...dn" attribute (and the same issue with ds)?
>
>
> Thanks very much,
>
> Marcus G.
>
> 	[[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099